RetrogeneDB ID: retro_ecab_788

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:55178416..55179341(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ATP5A1
• Ensembl ID: ENSECAG00000021561
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle [Source:HGNC Symbol;Acc:823]

Sequence

>retro_ecab_788
CTCCCTCTGCAGGCCAGTCTGGTCTCCAAAAATGCTTTGGGATCTTCTTTGATTGTCACAAGGAACCTCCTTGCCTCTAA
CACTTGTCTTCAGAAGGCTGGCACTGCCAAGGTGTCCTCTGTTCTCAAAGGGTGTATTCTTGGAGCTAATACCTCTGTTG
CCCTTGAAGAGACTGGATGTGTCTCAAGTATTGATGGTGGTATTGCTCGAGTACATGGGCTGAGGAATGTTCAAGCAGAA
GAAAGCATAGAATTTTTTTCAGGCTTAAAGGGTATGTCTCTGAACTTGGAACCTGACAATGCTGTTGTTGTTGTGTTTGG
AAACAATAAACTAATTAAGGAAGGAAATATTATGAAGAGTGCAGGAGCCATTGTGGGCATTCTAGTTGGTGAGAAACTGT
TGGGTCATGCAGTAGATGCCCTTGGTAATGTTATTGATGGAAAGGGTCCAGTTGGTGCCAAGACCTGTAGGTGAGTTGGC
CTGAAAGCCCTTGGGATCATTCCTCCAAACTCTGTGCAGGAACCAATGCAGATGGGCATTAATGCTGTGGATAGCTTGGT
GCCAATTTGTCGTGGTCAGCCTGAGCTGATTGTCGGTGACCGACAGACTGGCAAAACATCAATGATTGACAAGATCATTA
GCCAGAAATGTTTCAATGATGAATCTGATGAAAAGAAGAAGCTATACTGTATCTACATTTCTATTGGTCAAAAGAGATCC
ACTGTTGCCCAATTGGTGAAGAGACTTACAGATACCATGAAGTACACCATTGTGGTTTTAGCTACTGCTTCTGATGCTGG
CCCACATCAGTACCTGACTCCTTATTCTGCCTTTCTATGGGAGAAAATTTAGAGATAATGGCAAACATGCTTTGATCATC
TATGACGAGTTATCCAGATAGACTATTGCTTATTGTCAGATGTCT

Alignment

ORF - retro_ecab_788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.84 %
• Parental protein coverage: 56.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LPRRAGLVSRNALGSSFIAARNLHASNTRLQKTGTAEMSSILEERILGADTSVDLEETGRVLSIGDGIAR
          LP..A.LVS.NALGSS.I..RNL.ASNT.LQK.GTA..SS.L...ILGA.TSV.LEETG.V.SI..GIAR
Retrocopy LPLQASLVSKNALGSSLIVTRNLLASNTCLQKAGTAKVSSVLKGCILGANTSVALEETGCVSSIDGGIAR

Parental  VHGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDVPVGEELLGRVVDA
          VHGLRNVQAEE..EF.SGLKGMSLNLEPDN..VVVFGN.KLIKEG.I.K..GAIV...VGE.LLG..VDA
Retrocopy VHGLRNVQAEESIEFFSGLKGMSLNLEPDNAVVVVFGNNKLIKEGNIMKSAGAIVGILVGEKLLGHAVDA

Parental  LGNAIDGKGPIGSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
          LGN.IDGKGP.G.KT.R.VGLKA.GIIP..SV.EPMQ.GI.AVDSLVPI.RGQ.ELI.GDRQTGKTS..I
Retrocopy LGNVIDGKGPVGAKTCR*VGLKALGIIPPNSVQEPMQMGINAVDSLVPICRGQPELIVGDRQTGKTSM-I

Parental  DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQYLAPYSG
          D.II.QK.FND..DEKKKLYCIY..IGQKRSTVAQLVKRLT..D.MKYTIVV.ATASDA.P.QYL.PYS.
Retrocopy DKIISQKCFNDESDEKKKLYCIYISIGQKRSTVAQLVKRLT--DTMKYTIVVLATASDAGPHQYLTPYSA

Parental  -CSMGE-YFRDNGKHALIIYDDLSKQAVAYRQMS
          ..SMGE..FRDNGKHALIIYD.LS....AY.QMS
Retrocopy <LSMGE<KFRDNGKHALIIYDELSR*TIAYCQMS

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	0.00 RPM	252.88 RPM
SRP021940_cerebellum	0.05 RPM	814.25 RPM
SRP021940_embryo	0.10 RPM	610.24 RPM
SRP021940_placental_villous	0.00 RPM	390.90 RPM
SRP021940_synovial_membrane	0.05 RPM	310.76 RPM
SRP021940_testis	0.13 RPM	427.59 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_788 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_788 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_788 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002507	2 retrocopies	retro_btau_1380, retro_btau_1426,
Canis familiaris	ENSCAFG00000017648	2 retrocopies	retro_cfam_1483, retro_cfam_516,
Dasypus novemcinctus	ENSDNOG00000006331	2 retrocopies	retro_dnov_1740, retro_dnov_2525,
Equus caballus	ENSECAG00000021561	1 retrocopy	retro_ecab_788 ,
Homo sapiens	ENSG00000152234	1 retrocopy	retro_hsap_1702,
Gorilla gorilla	ENSGGOG00000016560	1 retrocopy	retro_ggor_1275,
Meleagris gallopavo	ENSMGAG00000009963	1 retrocopy	retro_mgal_14,
Microcebus murinus	ENSMICG00000017500	1 retrocopy	retro_mmur_1210,
Myotis lucifugus	ENSMLUG00000009856	1 retrocopy	retro_mluc_1198,
Macaca mulatta	ENSMMUG00000003570	1 retrocopy	retro_mmul_1208,
Mustela putorius furo	ENSMPUG00000000923	1 retrocopy	retro_mputfur_601,
Nomascus leucogenys	ENSNLEG00000010973	1 retrocopy	retro_nleu_1334,
Oryctolagus cuniculus	ENSOCUG00000003967	1 retrocopy	retro_ocun_1235,
Pongo abelii	ENSPPYG00000009130	1 retrocopy	retro_pabe_1363,
Pan troglodytes	ENSPTRG00000009991	1 retrocopy	retro_ptro_1151,
Sarcophilus harrisii	ENSSHAG00000017177	1 retrocopy	retro_shar_109,
Tarsius syrichta	ENSTSYG00000007804	1 retrocopy	retro_tsyr_1186,
Tursiops truncatus	ENSTTRG00000005118	1 retrocopy	retro_ttru_159,