RetrogeneDB ID: retro_ecab_72

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 14:35675943..35676741(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000005542
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000007666
• Aliases: None
• Description: None

Sequence

>retro_ecab_72
ATGCAGACGTTTCCCGCCCTGTACAAGGGCCTCACCGACTGCTGCCTCAAGACCTACTCCCAAGTGGGCTTGCGGGGCTT
CTACAAGGGGACTGGTCCAGCGCTCATTGCCTATGTCGCCCAGAACTCGGTCCTCTTCATGTGCTACGGCTTCTGCCAAC
AGTTTGTGAGGAAAGTGGTTGGACTGGACAAGCAGGCAAAACTGAGTGATCTGCAGACTGCAACCGCCGGTTCCTTCGCC
TCTGCGTTTGCTGCGCTCGCCCTGTGCCCCACTGAGCTTGTGAAGTGCCGGCTACAGACCATGCACGAAATGGAGATGTC
AGGGAAGATAGCAAAAAGCCATAATACAGTTTGGTCCGTCGTGAAGAGCATCCTTAGAAAGGATGGCCCCTTGGGCTTCT
ACCACGGACTCTCGAGCACTCTAATTCAAGAAATACCGGGCTATTTCTTCTTCTTCGGTGGCTATGAACTGAGCCGATCG
TTTTTTGCCTCAGGGAGATCGAAAGATGAACTAGGCCCTGTCCCTTTGATGTTAAGTGGTGGAATTGCTGGAATTTGCCT
TTGGGGTGTCATATACCCAGTGGATTGTATCAAATCCAGAATTCAGGTTCTTTCCATATCTGGAAAACAGGCAGGATTTA
TCGGAACTCTTCTAAGTGTTGTGAAAAATGAAGGAATAGCAGCCTTATATTCTGGACTGCAAGCTACTATGATTCGAGCG
TTCCCTGCCAATGGGGCACTATTTTTGGCTTATGAATACAGCAGGAAGATGATGATGGGCCAGTTTGAAGCATACTAA

Alignment

ORF - retro_ecab_72 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLHNAAAGSFASAFAALVLCPTELVKCRLQTMYETQMSGKIAKSQNTVWSVVKSILRKDGPLGFYHGLSS
          DL..A.AGSFASAFAAL.LCPTELVKCRLQTM.E..MSGKIAKS.NTVWSVVKSILRKDGPLGFYHGLSS
Retrocopy DLQTATAGSFASAFAALALCPTELVKCRLQTMHEMEMSGKIAKSHNTVWSVVKSILRKDGPLGFYHGLSS

Parental  TLLREVPGYFFFFGGYELSRSFFASGRSKDELGPVPLMLSGGVGGICLWLAVYPVDCIKSRIQVLSMSGK
          TL..E.PGYFFFFGGYELSRSFFASGRSKDELGPVPLMLSGG..GICLW...YPVDCIKSRIQVLS.SGK
Retrocopy TLIQEIPGYFFFFGGYELSRSFFASGRSKDELGPVPLMLSGGIAGICLWGVIYPVDCIKSRIQVLSISGK

Parental  QAGFLGTFITVVRNEGIMALYSGLKPTMIRAFPANGALFLAYEYSRRLMMSQFEAY
          QAGF.GT...VV.NEGI.ALYSGL..TMIRAFPANGALFLAYEYSR..MM.QFEAY
Retrocopy QAGFIGTLLSVVKNEGIAALYSGLQATMIRAFPANGALFLAYEYSRKMMMGQFEAY

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	0.06 RPM	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.10 RPM	0.61 RPM
SRP021940_placental_villous	0.00 RPM	0.10 RPM
SRP021940_synovial_membrane	0.27 RPM	0.74 RPM
SRP021940_testis	9.66 RPM	0.26 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_72 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_72 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_72 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Oryctolagus cuniculus	retro_ocun_192

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017797	1 retrocopy	retro_cjac_1776,
Cavia porcellus	ENSCPOG00000005570	2 retrocopies	retro_cpor_105, retro_cpor_107,
Equus caballus	ENSECAG00000007666	1 retrocopy	retro_ecab_72 ,
Homo sapiens	ENSG00000102743	1 retrocopy	retro_hsap_44,
Gorilla gorilla	ENSGGOG00000025261	1 retrocopy	retro_ggor_2294,
Microcebus murinus	ENSMICG00000007218	1 retrocopy	retro_mmur_18,
Macaca mulatta	ENSMMUG00000022585	1 retrocopy	retro_mmul_199,
Nomascus leucogenys	ENSNLEG00000001185	1 retrocopy	retro_nleu_1704,
Otolemur garnettii	ENSOGAG00000009380	1 retrocopy	retro_ogar_490,
Pongo abelii	ENSPPYG00000005307	1 retrocopy	retro_pabe_82,
Pan troglodytes	ENSPTRG00000005809	1 retrocopy	retro_ptro_2303,
Pteropus vampyrus	ENSPVAG00000010393	1 retrocopy	retro_pvam_15,
Ictidomys tridecemlineatus	ENSSTOG00000007840	1 retrocopy	retro_itri_726,
Tupaia belangeri	ENSTBEG00000017239	1 retrocopy	retro_tbel_4583,