geneid eXtended output format (Description)

Gene extracted from a human prediction (geneid eXtended format)
# Gene 7 (Reverse). 3 exons. 476 aa. Score = 47.50
    Stop    91832    91834       0.00   -       ATAA
Terminal    91832    92551      30.56   - 0 0   0.00  3.93   84.26  0.00   AA 237:476 gene_7
Acceptor    92551    92552       3.93   -       GCGGTGGTGCGGCTGTCCCCGCAGGTG
   Donor    93982    93983       1.23   -       AAGGTATCT
Internal    93983    94263       9.83   - 2 0   1.23  2.79   32.30  0.00   AA 143:236 gene_7
Acceptor    94263    94264       2.79   -       AGCTGTGAACTGTTTGTTTGCTAGGGT
   Donor    95208    95209       2.52   -       AAGGTAACC
   First    95209    95635       7.11   - 0 1   2.52  -1.55  30.08  0.00   AA   1:143 gene_7
   Start    95633    95635      -1.55   -       TTTAGAAAGCTGAGATGATG

>L1084|geneid_v1.1_predicted_protein_7|476_AA
MMERIRKEMILMERGLHSPTAGKRFSSLSDSAGGAVLEALENSQHPARLSPRLPSAPLHG
ALGDLPAKGKFEIDTLFNLQHPSSESTVSSEIASATESRKKPSHYSEAAAEADMSSDVEV
GCSALRSPSGLGAAPLKENNAKGYTESGSVAGTTTSASGSGLGSLHGGGGGGNSGAAALG
GSGSGSGADQVRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQ
NRRMKDKRQRLAMSWPHPADPSFYTYMMTHAAATGSLPYPFHSHVPLHYYPHVGVTAAAA
AAAASGAAAAASSPFATSIRPLDTFRALSHPYSRPELLCSFRHPGLYQAPAAAAGLNSAA
SAAAAAAAAAAAASSAAAAGAPPSGSSAPCSCLSCHSSQSAAAAAAAAAAALGSRGGGGS
GGGGGGGAGTAGGSDFGCSAAAPRSESGFLPYSAAVLSKTAVSPPDQRDEAPLTR*


Description of columns (geneid eXtended format)
Exon type Type of predicted exon: First, Internal, Terminal or Single
Signal type Type of predicted signal: Acceptor, Donor, Start or Stop codon
Positions Start and finish positions of current exon and signals
Score Score (reliability) of exon and signals
Strand Reading sense: forward or reverse
Frame Left uncomplete codon length in this exon
Remainder Right uncomplete codon length in this exon
Partial scores (exons): Scores (log likelihood) from:
  • Score for both signals defining exon
  • Protein coding potential (exon content)
  • Homology information score (SR regions): provided by user
AA Amino acids corresponding to the exon translation
Key Gene identifier



Enrique Blanco Garcia © 2003