RetrogeneDB ID: retro_ecab_997

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:51653862..51655594(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARHGAP42
• Ensembl ID: ENSECAG00000005829
• Aliases: None
• Description: Rho GTPase activating protein 42 [Source:HGNC Symbol;Acc:26545]

Sequence

>retro_ecab_997
CAAAGGATGAAATCTGCCAGCCAAGATTCCAGACCCCCCAGCCAGGGAATGATGGAAGGCTATCTTTACATCCAGGAGAA
ATGACCGCTTCATTTTACATGGATTAAACATTATTGTACACACGATAAGGGAGGTAAAACATTTACAAAGAGCATTTCAG
AAATGCAATCCAGTGGGGAAGTGAATGGCCTTATTACCAGCTCACCAGAAATGTCTAAATTAAAGTCTGGTATCCAACTA
AGGACAGACTCAATTGACAAATGATTCTGCTTTGACATGGAAGTAGTTGACAGGCATGGGAGCACCACATTGCAGGCCGT
CTCAGAAGCTAATCGGAAATCCTGGCTTAAAGTCATGGATGGGAAGGAATTGATTCACACCCTGCCTGCCATTACCAGCA
AGAAAGAAGAAATGTACCTAAATGAAGCAGGGTTCAACTTTGTAAGAAAATGCATTCAAGCTGTGGAAACAAGAGGCATC
ACCGTTTTAGGCCTGTAACGAATAGGAGGCGTGAACTCCGAAGTTCAGAGACTCACGAATACCACATCTTCTTCAAAATC
CCCTCCTGATATTGACATTGATATTGAACTATGAGATAATAAGACAATAACAAGTCGGCTGAAAAATGACCTCAGGTGCC
TTGCATAACCACTGATGACTTACAACTTACACAAAGATTTGATTGTTGCTGTTAACTCCGATGACCAGAACTTCCAGGTG
GATGCATTGGTGCACAATTGCCAGAGAAAAACAGAGAGATGCTGGAAATCTTAATAAAGCACCTGGTCAAAGTATCACTA
CACAGCCAATAAAATCTTATGACTGTCTCAAACCTTGGTTTCACATTCGGCCCAACTCTAATTGAGAGCACAGGAAGAAA
CTGTGGCTGCCATAATGAATATTAAATGTCAGAATATGGTGGTTGAAATTCTGGTAGAACACTATGAAAAGATTTTTCAT
ACTGCCGCAGACCCAAGCATTGCTCTTCCTCAGCTTCAGTCTTGATATGCATCCTGAAGGACAGGAGCAGCCTGCCTCTC
CACAGGCTCCCGGAAGCCCAGAAGGAGGTATACTCCATGCCTGGCAGAACACTATAGGGACTCCTATAGCGGCAGCCCAG
ACAGCACACCCACAGGGAGCGAATCACTCTTCTCTCACTCCTCCGAACAAAACAGCACTACAATGTCAGCTTCCTGCCAG
CCCAGGGAAAAATCTGGAGGGATTCCGTCATTGCATCCCCATCACCTCCCAATGGACGGAAGAGTCTTGGTCTGTGGACT
AGTCCTGAATCAAGTTCTAGAGCAGATGTAACCAAAACAGATGCAGAATCAGATTACCATACGGTTGCCTCCCTCACTAG
CCCAGGATATGTTTCCCCACCCACAGACCTGACCAAGAAAGGGCCCTATGGACTTTCAGGACCGAAAAGAGCCTCAGCTT
CCTCTCTCTGATCCCTCTCTGCTGCTAAAGGAAGCAAGAGCTACAGTGGATCCATTCAAAGCTTAACTTCCATAGGTTCC
AAAGAGACACCCAAAGCCCCACCAAACCCAGGCCAGCCTCCAAAAATGTGCGGGAGATTAAAGCTAAACACTGTCTTAAG
CAATGGCTACCAGCGCCTTGGCTCCATTGTAGCAACGAAAGCGCAACTCTTTGAAACAGTGGTTCCCTTCAGCCAGTTTC
TTCCGGGCGGCGGCAAGTGAAAGCCACGTACGCCTGCAAAGCAGAGCACAGC

Alignment

ORF - retro_ecab_997 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.88 %
• Parental protein coverage: 99.14 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QRMKSANQDYRPPSQWTMEGYLYVQEKRPLGFTWIKHYCTYDKGSKTFTMSVSEMKSSGKMNGLVTSSPE
          QRMKSA.QD.RPPSQ..MEGYLY.QEK.PL.FTWIKHYCT.DKG.KTFT.S.SEM.SSG..NGL.TSSPE
Retrocopy QRMKSASQDSRPPSQGMMEGYLYIQEK*PLHFTWIKHYCTHDKGGKTFTKSISEMQSSGEVNGLITSSPE

Parental  MFKLKSCIRRKTDSIDKRFCFDIEVVERHGIITLQAFSEANRKLWLEAMDGKEPIYTLPAIISKKEEMYL
          M.KLKS.I...TDSIDK.FCFD.EVV.RHG..TLQA.SEANRK.WL..MDGKE.I.TLPAI.SKKEEMYL
Retrocopy MSKLKSGIQLRTDSIDK*FCFDMEVVDRHGSTTLQAVSEANRKSWLKVMDGKELIHTLPAITSKKEEMYL

Parental  NEAGFNFVRKCIQAVETRGINILGLYRIGGVNSKVQKLMNTTFSPKSPPDIDIDIELWDNKTITSGLKNY
          NEAGFNFVRKCIQAVETRGI..LGL.RIGGVNS.VQ.L.NTT.S.KSPPDIDIDIEL.DNKTITS.LKN.
Retrocopy NEAGFNFVRKCIQAVETRGITVLGL*RIGGVNSEVQRLTNTTSSSKSPPDIDIDIEL*DNKTITSRLKND

Parental  LRCLAEPLMTYKLHKDFIVAVKSDDQNYRVEAVHALVH-KLPEKNREMLDILIKHLVKVSLHSQQNLMTV
          LRCLA.PLMTY.LHKD.IVAV.SDDQN..V.A...LVH..LPEKNREML.ILIKHLVKVSLHSQ.NLMTV
Retrocopy LRCLA*PLMTYNLHKDLIVAVNSDDQNFQVDA---LVH<QLPEKNREMLEILIKHLVKVSLHSQ*NLMTV

Parental  SNLGVIFGPTL-MRAQEETVAAMMNIKFQNIVVEILIEHYEKIFHTAPDPSIPLPQPQSRSGSRRTRAIC
          SNLG..FGPTL..RAQEETVAA.MNIK.QN.VVEIL.EHYEKIFHTA.DPSI.LPQ.QS...S.RT.A.C
Retrocopy SNLGFTFGPTL>LRAQEETVAAIMNIKCQNMVVEILVEHYEKIFHTAADPSIALPQLQS*YAS*RTGAAC

Parental  LSTGSRKPRGRYTPCLAEPDSDSYSSSPDSTPMGSIESLSSHSSEQNSTTKSASCQPREKSGGIP-WIAS
          LSTGSRKPR.RYTPCLAE...DSYS.SPDSTP.GS.ESL.SHSSEQNSTT.SASCQPREKSGGIP..IAS
Retrocopy LSTGSRKPRRRYTPCLAEHYRDSYSGSPDSTPTGS-ESLFSHSSEQNSTTMSASCQPREKSGGIP<VIAS

Parental  PSPSNGQKNLGLWTTSPESSSREDATKTDAESD----CQITSPGDTSPPIDLTKKGPYGLSGLKRASASS
          PSP.NG.K.LGLW.TSPESSSR.D.TKTDAESD.......TSPG..SPP.DLTKKGPYGLSG.KRASASS
Retrocopy PSPPNGRKSLGLW-TSPESSSRADVTKTDAESDYHTVASLTSPGYVSPPTDLTKKGPYGLSGPKRASASS

Parental  LRSISAAEGNKSYSGSIQSLTSIGSKETPKAAPNPDLPPKMCRRLRLDTASSNGYQRPGSVVAAKAQLFE
          L.S.SAA.G.KSYSGSIQSLTSIGSKETPKA.PNP..PPKMC.RL.L.T..SNGYQR.GS.VA.KAQLFE
Retrocopy L*SLSAAKGSKSYSGSIQSLTSIGSKETPKAPPNPGQPPKMCGRLKLNTVLSNGYQRLGSIVATKAQLFE

Parental  -NVGSLKPVSSG-RQAKAMYSCKAEHS
          .N.GSL.PVSSG.RQ.KA.Y.CKAEHS
Retrocopy <NSGSLQPVSSGRRQVKATYACKAEHS

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	0.47 RPM
SRP021940_cerebellum	0.00 RPM	1.45 RPM
SRP021940_embryo	0.00 RPM	12.02 RPM
SRP021940_placental_villous	0.00 RPM	9.14 RPM
SRP021940_synovial_membrane	0.00 RPM	5.46 RPM
SRP021940_testis	0.00 RPM	1.85 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_997 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_997 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_997 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000005829	1 retrocopy	retro_ecab_997 ,
Homo sapiens	ENSG00000165895	2 retrocopies	retro_hsap_2156, retro_hsap_2318,
Gorilla gorilla	ENSGGOG00000011397	2 retrocopies	retro_ggor_1714, retro_ggor_1758,
Pongo abelii	ENSPPYG00000003799	1 retrocopy	retro_pabe_2095,
Pan troglodytes	ENSPTRG00000004204	4 retrocopies	retro_ptro_1641, retro_ptro_1692, retro_ptro_3083, retro_ptro_892,