RetrogeneDB ID: retro_ecab_560

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:230586..231731(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000021667
• Aliases: None
• Description: None

Sequence

>retro_ecab_560
GACTTGGTGGCCATTTAGGATGTGGCTGTGAACTTCACCCTGAAGGAGTGGGCTTTACTGGGTCCTTCATAGAAGAAACT
CTACAGAGATGTGATGTGAGAAACCTTCAGGAACCAGGCCTCAATAGGAAAAACATGGGAAGGTCATGATATTGAAGATC
AGTACAAAAACCAGGGTAGAAAACGAAGAAGTCATATGGTAAGGAGTCTGTGAAAGTGAAGAGAGTACTCAATGCAGAAA
ACATTTCAGCCTCATTCCAAATCTCAATCTGACAAGAAAACTACAGGAGCTAAACCATGTGAATGATGTGCATGTGGGAA
ACTCTTTGTGCGTCATGCATCCCTTAACAGGCACCTTAGAGTCACACTGAATCCACACCATATGACTATCAACAATATGG
AGAGAAGCCATATACGTGTAAGGAAGGTGGTTTCACTCTTACCAGTTTTCTTCAAATACATGAAAGAACTCATACTGGAG
AGAAACCCTATGAATGTAAAAAATGCAGTAATGCGTTCACTTCTTCCAGTTCTCTTTAAGTCCATGAAAGGATTCATACT
GGAGACAAACTCTATAAATGTAAAAACTGTGGGAAAGCCTTTATAGCTCCCTCAAGCCTTTGATCACACATGATCTTTCA
CACTGGAGATGGACCTTATAAAAGTAAGGAATGTGAGAAAGTGTTCATTTCTTCCAGTGCATTTCAAGTACATGAAAGGA
GTCACAGTGGAGAGAAACCCTACGAATGTAAAGATTGCAGTAACACATGCAGTCATTCCAGTACACTTTGAATATACGAA
AGACGTCACACTGGAGAGAAACCCTATGAATGTGAAGAATGTGAGAAAGCCTTAAGTTCTCATCAAAGTTTCCAAATACA
TAAAAGAAGTCATACAGGAGAGAAACGATATGAATTTAAAAATGTAGCAAAGCTTTTAATTTTCCCAGTTCTCTTCAAAG
ACATGAAATAACTCACATGGGAGAGAAACCCTGTGAATGTCAGTAAAGTGGGAAGGCCTTTATTTTTCATGCAAACTTTC
AAGGATATACAAGAAAGCATACTAGAGGAAAAACCAATTAAATATAATGGATGCGGGAAAGGCTTTCATCATCACAGTTC
TTTCTGAAGGCATAAAAGGAGTCAC

Alignment

ORF - retro_ecab_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 54.38 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DSVAIEDVTVSFTLEEWALLDPSQKKLYRDVMWETFRNLASVGKTWEDHDIEEKYQKQERKLRSHMVER-
          D.VAI.DV.V.FTL.EWALL.PS.KKLYRDVM.ETFRN.AS.GKTWE.HDIE..Y.K.....R.....R.
Retrocopy DLVAI*DVAVNFTLKEWALLGPS*KKLYRDVM*ETFRNQASIGKTWEGHDIEDQY-KNQGRKRRSHMVR>

Parental  LCESEEGGQCGENFSLLPNLKLK-KKPTAAKPYKCSACGKVFMHHSSLNRHVRC-HNEHRPHAYQKCAEK
          .CESEE..QC...FSL.PNL.L..KK.T.AKP....ACGK.F..H.SLNRH.R..H.E..P..YQ...EK
Retrocopy VCESEESTQCRKHFSLIPNLNLT<KKTTGAKPCE*CACGKLFVRHASLNRHLRV<HTESTPYDYQQYGEK

Parental  PYKCKECGKAFPFPSSLQIHERTHTGEKPYECKNCGKAFISSKSLRIHERIHTGEKPYECKECGKAFTAP
          PY.CKE.G..F...S.LQIHERTHTGEKPYECK.C..AF.SS.SL..HERIHTG.K.Y.CK.CGKAF.AP
Retrocopy PYTCKEGG--FTLTSFLQIHERTHTGEKPYECKKCSNAFTSSSSL*VHERIHTGDKLYKCKNCGKAFIAP

Parental  SSLRSHMISHTGDGPYKCKECRKVFISPSAFRIHERSHTGEKPYECKNCGKAFTSSKSLRIHERIHTGEK
          SSL.SHMI.HTGDGPYK.KEC.KVFIS.SAF..HERSH.GEKPYECK.C......S..L.I.ER.HTGEK
Retrocopy SSL*SHMIFHTGDGPYKSKECEKVFISSSAFQVHERSHSGEKPYECKDCSNTCSHSSTL*IYERRHTGEK

Parental  PYECKECGKAFTAPSSLRLHMISHTGDGPYKCK-ECKKVFISPSAFQIHERSHTGEKPYECKYCGKAFIS
          PYEC.EC.KA.....S...H..SHTG...Y..K..C.K.F..PS..Q.HE..H.GEKP.EC...GKAFI.
Retrocopy PYECEECEKALSSHQSFQIHKRSHTGEKRYEFK<KCSKAFNFPSSLQRHEITHMGEKPCECQ*SGKAFIF

Parental  SSSFQIHERSHT-GEKPYECKECGKAFSLYANLKKHQKTH
          ...FQ...R.HT..EKP.....CGK.F........H...H
Retrocopy HANFQGYTRKHT>EEKPIKYNGCGKGFHHHSSF*RHKRSH

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	0.77 RPM
SRP021940_cerebellum	0.00 RPM	0.21 RPM
SRP021940_embryo	0.03 RPM	1.76 RPM
SRP021940_placental_villous	0.00 RPM	0.96 RPM
SRP021940_synovial_membrane	0.00 RPM	0.66 RPM
SRP021940_testis	0.00 RPM	0.38 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_560 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_560 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008838	1 retrocopy	retro_acar_51,
Anolis carolinensis	ENSACAG00000023302	2 retrocopies	retro_acar_3, retro_acar_34,
Anolis carolinensis	ENSACAG00000026389	2 retrocopies	retro_acar_13, retro_acar_4,
Anolis carolinensis	ENSACAG00000026721	1 retrocopy	retro_acar_23,
Anolis carolinensis	ENSACAG00000026996	1 retrocopy	retro_acar_22,
Anolis carolinensis	ENSACAG00000027062	1 retrocopy	retro_acar_29,
Ciona savignyi	ENSCSAVG00000007589	2 retrocopies	retro_csav_30, retro_csav_31,
Equus caballus	ENSECAG00000010608	1 retrocopy	retro_ecab_68,
Equus caballus	ENSECAG00000021667	1 retrocopy	retro_ecab_560 ,
Equus caballus	ENSECAG00000023688	1 retrocopy	retro_ecab_75,
Macaca mulatta	ENSMMUG00000013571	1 retrocopy	retro_mmul_248,