RetrogeneDB ID: retro_ecab_866

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:75335651..75336573(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000024825
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GTF3A
• Ensembl ID: ENSECAG00000014803
• Aliases: None
• Description: general transcription factor IIIA [Source:HGNC Symbol;Acc:4662]

Sequence

>retro_ecab_866
AGACCATTTGTCTGTGACCGTGAAGGGTGTGGCAAAGCCCTTTGTCAGGGACTACCGTCTGAGCGGCCACATCCTGATTC
ACACTGGAGAAAAGCCATTTGGTTTGTGCAGCTAGTGGCTGTGATCAAAAATTTCAACACAAAGTCAAACTTGGAGGAAA
CCATTTTGGAACGCAAACATGAAAATCCGCAGAAACAGTATGTATGCAGTTTTTGAAAGGTTGGTGAGAAGACCTTTAGG
AAACAAGCAGCAGCTGAACATCCATCAGTGCCAGCACACCAACGGACCACTGTTTAAGTGTACCCATGAAGGATGTGGAA
AGCACTTCGCTTCTCCCCGTGGGCTGAAACGGCAGGGGAAGGTCCACGAGGGTTATATATGTCAAAAAGAATGTTCCTTC
GTGGCAAAAACATGGACAGAGCTTCTGAAACATGTGAGAGAAGCCCATCAAGGGGAGATAAGATGTGAAGTATGCCAGAA
AACATTTAAACGCAAAGATTATCTGAAGCAACATAAGAAAACTGATGCCCCGGAGTGGGATGTGTGTCGATGTCCAAGAG
AAGGCTGTGATAGAACCTACACAACCGTGTCTAATCTCCAGAGCCATATTCTCTCTTTTCATGAGGAAAGGTGCCCGTTT
ACACGTGAACATGCTGGCTGTGGCAAGACGTTTGCAATGAAGCAAAGTCTCACTAGGCATGCCGTCGCACATGACCCTGA
CAAGAAAATGAAGCTCAAAGTAAAACCTACTCGAGAAAAGCGGAGTTTGGCCTCTCGTGTCAGTGGATATATCCCTCCTA
AAAAGAAACAAGAACAAGGCGTATCTCTGCCAACAAACGGAGAGTCACTGCGCTGCCCTCCAGACCGGGCGCCCCTGACC
ATTGCAGTGCTCGCCCTCAGCCAGAGAGCATCTTGCTTTGTT

Alignment

ORF - retro_ecab_866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RPFVCDHEGCGKA-FVRDYHLSRHILIHTGEKPF-VCAASGCDQKF-NTKSNLRKHF-ERKHENQQKQYV
          RPFVCD.EGCGKA.FVRDY.LS.HILIHTGEKPF.VCAASGCDQKF.NTKSNL.....ERKHEN.QKQYV
Retrocopy RPFVCDREGCGKA>FVRDYRLSGHILIHTGEKPF>VCAASGCDQKF>NTKSNLEETILERKHENPQKQYV

Parental  CSF-EGCEKTFRKH-QQLKIHQCQHTNEPLFKCTHEGCGKHFASPSGLKRHGKVHEGYICQKECSFVAKT
          CSF....EKTFRK..QQL.IHQCQHTN.PLFKCTHEGCGKHFASP.GLKR.GKVHEGYICQKECSFVAKT
Retrocopy CSF*KVGEKTFRKQ>QQLNIHQCQHTNGPLFKCTHEGCGKHFASPRGLKRQGKVHEGYICQKECSFVAKT

Parental  WTDLLKHVREAHQEEIRCEVCQKTFKRKDYLKQHMKTHAPERDVCRCPREGCDRTYTTVFNLQSHILSFH
          WT.LLKHVREAHQ.EIRCEVCQKTFKRKDYLKQH.KT.APE.DVCRCPREGCDRTYTTV.NLQSHILSFH
Retrocopy WTELLKHVREAHQGEIRCEVCQKTFKRKDYLKQHKKTDAPEWDVCRCPREGCDRTYTTVSNLQSHILSFH

Parental  EERRPFTCEHAGCGKTFAMKQSLTRHAVVHDPDKKKMKLKVKPSREKRSLASRLSGYIPPKKKQEQGVSL
          EER.PFT.EHAGCGKTFAMKQSLTRHAV.HDPD.KKMKLKVKP.REKRSLASR.SGYIPPKKKQEQGVSL
Retrocopy EERCPFTREHAGCGKTFAMKQSLTRHAVAHDPD-KKMKLKVKPTREKRSLASRVSGYIPPKKKQEQGVSL

Parental  PTNGESLRCPPDQVPLTAAVLALSQRAACFV
          PTNGESLRCPPD..PLT.AVLALSQRA.CFV
Retrocopy PTNGESLRCPPDRAPLTIAVLALSQRASCFV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP021940_articular_cartilage	0.53 RPM	13.58 RPM
SRP021940_cerebellum	0.78 RPM	31.00 RPM
SRP021940_embryo	1.00 RPM	44.09 RPM
SRP021940_placental_villous	0.63 RPM	27.09 RPM
SRP021940_synovial_membrane	0.69 RPM	29.59 RPM
SRP021940_testis	17.39 RPM	103.08 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_866 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_866 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_866 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019373	1 retrocopy	retro_cjac_3066,
Equus caballus	ENSECAG00000014803	1 retrocopy	retro_ecab_866 ,
Equus caballus	ENSECAG00000026954	2 retrocopies	retro_ecab_1064, retro_ecab_1107,
Felis catus	ENSFCAG00000006982	1 retrocopy	retro_fcat_426,
Gasterosteus aculeatus	ENSGACG00000003107	1 retrocopy	retro_gacu_6,
Gorilla gorilla	ENSGGOG00000008407	1 retrocopy	retro_ggor_2622,
Microcebus murinus	ENSMICG00000014763	1 retrocopy	retro_mmur_368,
Macaca mulatta	ENSMMUG00000009029	1 retrocopy	retro_mmul_1632,
Nomascus leucogenys	ENSNLEG00000000331	2 retrocopies	retro_nleu_1134, retro_nleu_214,
Oreochromis niloticus	ENSONIG00000014134	1 retrocopy	retro_onil_8,
Vicugna pacos	ENSVPAG00000004995	1 retrocopy	retro_vpac_456,