RetrogeneDB ID: retro_ecab_516

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:61577889..61578994(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSRP1
• Ensembl ID: ENSECAG00000016612
• Aliases: None
• Description: structure specific recognition protein 1 [Source:HGNC Symbol;Acc:11327]

Sequence

>retro_ecab_516
CTTACAAGCAAGGCCTTTGACTACAAGATCTCCTACACTTCAGTACCTAATCTCTTTTTGTTGCGTCACAAGGACCATCA
CCAGATATTCTTTGTGATCAGGCTGTATCCCTCCATCAAGCAGGGCAAAACCTGGTACCGCTTCCTGATCCTCCTTTTCT
CCAAGGACAAGGACATTTCCTTGACTTCCAACAAGAACAAGGAAGAAATGGAGAAGCACTTTGATAGGCAGTTCACTAAG
AACATGTTGGGATCCCTCCAAGAGATGGTTGGCCAAGTCATGAAAGCATTGGTGAACCACAAGGTCACACTCCCAGGCAA
CTTCCAAGGACATTTAGGGGCCCAGTGTTTCACTTGCTCCTACAAGGTGAGCTCAGGACTGCTCTACCTGCTCAGTGGGG
CTTCATCTAGGTTCACAAGCCACCCAGACAGATCTGCTTTGACAAAATCTCTTTCATCAACTTTGCCAATGGCACCACTG
CCACTTGCTCCTTTGACTTTGAAATTGAGACCAAGCAGGCACTCAGTATACCTTCGGCAGCATTGAGAGGGAGGAGTATG
AGAAACCATTTGATTTTGTCAATGCAAAAAAGCTCAACATCAAAAACCAAATATTAAAAGAGAAGATGAACCAAAACTAC
AATGAATAGGCCTCTAACTCTGATGAAGATGAGTGTGATGTCTTCATGGAACTGATAAAAGATGCCTGCTTAGAGAATGC
CACCAAAAACTATAGTGACTCAGGAGAATAAACTGATAAGTCATTCTAGTCAGGTGGAGAAAAGCAGGAAATGGCAGAGA
AGTTTAACAGTAACGCCTCTGCCAGCCAGCTCTTCCAGTAATGATGGTGACAGTGATTGGGATGAGACGAAGAGAAAACA
GCTCAAAACAGCTGAAACAGTCAAGGATCACAATGGTCTCAAGAAGTCTGTGGAGGTGGAGAAGGGCAAAGTCCTCAATG
CCCCCAAAAGGCACATGTCTGCATACATGCTGTGCTCAATGCTACTTGAGAGAAGATCAAGCCTGCCCATCTTGGCATCA
GTATCATGGATATTTCCAAGAAGGCATACAAGATCTGGAAGGGGATGCCCAAGGAGAAGAAAGAG

Alignment

ORF - retro_ecab_516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.02 %
• Parental protein coverage: 62.29 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LHGKTFDYKIPYTTVLRLFLLPHKDQRQMFFVISLDPPIKQGQTRYHFLILLFSKDEDISLTLNMNEEEV
          L..K.FDYKI.YT.V..LFLL.HKD..Q.FFVI.L.P.IKQG.T.Y.FLILLFSKD.DISLT.N.N.EE.
Retrocopy LTSKAFDYKISYTSVPNLFLLRHKDHHQIFFVIRLYPSIKQGKTWYRFLILLFSKDKDISLTSNKNKEEM

Parental  EKRFEGRLTKNMSGSLYEMVSRVMKALVNRKITVPGNFQGHSGAQCITCSYKASSGLLY-PLERGFIYVH
          EK.F....TKNM.GSL.EMV..VMKALVN.K.T.PGNFQGH.GAQC.TCSYK.SSGLLY.P...GFI.VH
Retrocopy EKHFDRQFTKNMLGSLQEMVGQVMKALVNHKVTLPGNFQGHLGAQCFTCSYKVSSGLLY<PAQWGFI*VH

Parental  KPPVHIRFDEISFVNFARGTTTTRSFDFEIETKQ-GTQYTFSSIEREEYGKLFDFVNAKKLNIKNRGLKE
          KPP..I.FD.ISF.NFA.GTT.T.SFDFEIETKQ.GTQYTF.SIEREEY.K.FDFVNAKKLNIKN..LKE
Retrocopy KPPRQICFDKISFINFANGTTATCSFDFEIETKQ<GTQYTFGSIEREEYEKPFDFVNAKKLNIKNQILKE

Parental  GMNPNYDEYA-DSDEDQHDAYLERMKEEGKIREENANDSSDDSGEETDESFNPGEEEEDVAEEFDSNASA
          .MN.NY.E.A..SDED..D...E..K......E......SD.SGE.TD.SF..G.E....AE.F.SNASA
Retrocopy KMNQNYNE*ASNSDEDECDVFMELIKD--ACLENATKNYSD-SGE*TDKSF*SGGEKQEMAEKFNSNASA

Parental  S-SS-SNEGDSDRDEKKRKQLKKAKMAKDRKSRKKPMEVKKGKDPNAPKRPMSAYMLW-LNASREKIKSD
          S.SS.SN.GDSD.DE.KRKQLK.A...KD....KK..EV.KGK..NAPKR.MSAYML..LNA..EKIK..
Retrocopy S>SSSSNDGDSDWDETKRKQLKTAETVKDHNGLKKSVEVEKGKVLNAPKRHMSAYMLC<LNAT*EKIKPA

Parental  HPGISITDLSKKAGEIWKGMSKEKKE
          H.GISI.D.SKKA..IWKGM.KEKKE
Retrocopy HLGISIMDISKKAYKIWKGMPKEKKE

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	0.18 RPM	78.86 RPM
SRP021940_cerebellum	0.42 RPM	96.44 RPM
SRP021940_embryo	0.92 RPM	229.80 RPM
SRP021940_placental_villous	0.38 RPM	65.05 RPM
SRP021940_synovial_membrane	0.47 RPM	76.37 RPM
SRP021940_testis	0.51 RPM	82.36 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_516 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_516 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000375	1 retrocopy	retro_btau_1834,
Cavia porcellus	ENSCPOG00000000480	1 retrocopy	retro_cpor_70,
Equus caballus	ENSECAG00000016612	1 retrocopy	retro_ecab_516 ,