RetrogeneDB ID: retro_ecab_1057

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:35951530..35953408(+)
• Located in intron of: ENSECAG00000016627

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000010589
• Aliases: None
• Description: None

Sequence

>retro_ecab_1057
GCCAGTCCTCTTCTAGAAGAAATGGCTTCTCTAGAGGATGCCTACAGCTTTGAGGCTAATTCCAAACATAGTTCCCATAA
CTCCATGAACTCTGAATTTGCTGCCAAAGATGAGGATCAAAATTATAAGACTGAGGAACAAAACAAGGTCCAGAGAAGGA
TGGATAAACAGCGAGACCAGTGCTCTTCAGTGATCTGCATGAAGGCTATGCATGGCATCCTGGAAGAATTGATGCCACAA
GGAAGGGAAGAGGTTGCCGCTAGTGCAAAACTGAGCACAAGTGAGTGTCCCAATCCTGGAGAAAGACCAGCCAGGCTTGT
CACCTTCTCTGCTCGTCAGAAAAAGAAAGCATCAGCTCCCGAGTTCAGAGCAGAGAAGGAAAAGATAGTGATAGAGATCA
ACAGCAGCGGTGACAGGAGAGTGATTCTCGTTCCTCAGGAGAAACCCAGTGAGAAGCCAATTGGTGCCAGAAGGACAGTC
GCTTTTGAAAAAGGCTCTCTAGCCCTAGAATTTCTAGACAAACGTGACTTTCCTTTACAAATCCAACAGCATAGCGGAAG
GGATGTGGTGGTTGAGCACCTGTCTTCAGGAAGTGACTGGCCTGATGTGGATGAGATTTCCACAGTCACATTCTCTCAGG
AGGAGCTAGTCTCACTGAGTCTCTCAAGAGATCCAAAGTCTTCACTCTTCACCACTGTAGGTGACACATACCAGCCTCGT
TTGTACACTGGTCCTTGCTATGACTATGCCAGCTACTGGACCAGCACTCTCAAGCCTTTTCACTATCCCTCCTTGGGCCG
CAGCAGCAGCATGTCCCAGGCTGGGATGAGCACCGGGAGCTTCTTTAGTGATTATGCCTCCAGCTCTACAGTGCACTCCC
AAAACTGCTCCAGAGACCTCACGGCGGCAGAGAAAGGTCAGTCCCAGAATTCTCATTCATTTCATCTCTCCAGAAGTTCG
GAAGCAAAGGTGAAGGAGAAAAAAACATTCCAAGAGGAGACACCATCACGTCCTTGGGGAGGACATGCATCTGCTTCCCT
GCCGAGGAGCCAGCAGGAGCGAAGCTTACAGGAGGGTTTCATTGATACCCACTGTCACTTGGACATGCTCTTTTCCAAGT
TATCTTTCAAAGGGACCTTTAGGAAGTTCAGAAAAATTTATAGCCACTCCTTCCCTAAGGAATTTCAGGGCTGCATCTCT
GATTTCTGTGATCCTCGCACACTAAGCAATGGCCTATGGGAGGAGCTGTTGAAAGATGATCTGGTTTGGGGGGGCTTTGG
CTGTCACCCCCATTTTGCATGTTACTACAATGACATTCAAGAAAGAAATCTGTTGCAAGCCTTACGGCACCCCAAGGCTG
TAGTGTTTGGAAAAATGGGCTTGGATTACTCTCACAAGTGCACCATGCCTATCCCACAGCAGCACAAGGTATTTGAGAGG
CAGCTGAAGCTGGCTGTGTCTCTGAAGAAGCCCTTGGTGATCCACTGCCGGAACGCTGACGAAGATCTGCTGAGCATCAT
GAAGGCATTTGTGCCCTCTGACTACAAGATCCATAGGCATTGCTTCACTGGCAGCTACCCAGTCATCGAGCCACTTTTGA
AATACTTTCCCAACATGTCTGTGGGCTTCACAGCAGTCGTGACTTACTCTTCCGCCTGGGAGGTCCGCAATGCTCTGAAA
AAGATCCCGCTGGAGAGAATCATCGTGGAAACTGACGCTCCCTACTTCCTCCCTCGTGGGGTTCCTAAAAGAGTTTGCCA
GTATGCCCACCCAGGCCTGGCCCTGTATACAGTTCGAGAGATTGCCAGCATCAAAGAAGAGTCACTCTCACACACCTTGG
CCACCCTGCGTGAGAACACTAGTCGCCTCTACAGTCTT

Alignment

ORF - retro_ecab_1057 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.26 %
• Parental protein coverage: 84.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ANPSLEEMASLEEGACSLKVDSKDSSRNSMNSEFAAEAEGQNEVTEEPNKVQKRKRDRLRDQGSTVIYLK
          A.P.LEEMASLE..A.S....SK.SS.NSMNSEFAA..E.QN..TEE.NKVQ.R..D..RDQ.S.VI..K
Retrocopy ASPLLEEMASLED-AYSFEANSKHSSHNSMNSEFAAKDEDQNYKTEEQNKVQRRM-DKQRDQCSSVICMK

Parental  AIQGILGKSMPKRKGEAATRAKPGPGERPSCGEGPARSVSVSAPQKERESAPDVRAEEEKPVLEGSSFRD
          A..GIL...MP....E.A..AK....E.P..GE.PAR.V..SA.QK...SAP..RAE.EK.V.E..S..D
Retrocopy AMHGILEELMPQGREEVAASAKLSTSECPNPGERPARLVTFSARQKKKASAPEFRAEKEKIVIEINSSGD

Parental  RRVVIDPQENPTEEPLGDRRTV-IDKRSPPLEFLDDSDSHLESQKPKEREVVLEHTSSGSDWSDVDEIPT
          RRV...PQE.P.E.P.G.RRTV...K.S..LEFLD..D..L..Q....R.VV.EH.SSGSDW.DVDEI.T
Retrocopy RRVILVPQEKPSEKPIGARRTVAFEKGSLALEFLDKRDFPLQIQQHSGRDVVVEHLSSGSDWPDVDEIST

Parental  VRFSQEEPVSLKLPAVPEPSAFPTDYVMYPAHLYSSPWCDYASYWTSSPKPSSYPSVGSGSGNDTSQAGR
          V.FSQEE.VSL.L...P..S.F.T....Y...LY..P..DYASYWTS..KP..YPS.G..S....SQAG.
Retrocopy VTFSQEELVSLSLSRDPKSSLFTTVGDTYQPRLYTGPCYDYASYWTSTLKPFHYPSLGRSSS--MSQAGM

Parental  GSRGLLSDYPPNSTVSSHNASRDLVATEEGRSQNSRSSRFSRSSEEEELKERRTFQEETPLRPCGGHGSS
          ......SDY...STV.S.N.SRDL.A.E.G.SQNS.S...SRSSE....KE..TFQEETP.RP.GGH.S.
Retrocopy STGSFFSDYASSSTVHSQNCSRDLTAAEKGQSQNSHSFHLSRSSEAK-VKEKKTFQEETPSRPWGGHASA

Parental  SLPRSHREPSPEEGFIDTHCHLDMLYSKLSFKGTFTKFRKIYSSSFPKEFQGCISDFCDPRTLTDCLWEE
          SLPRS..E.S..EGFIDTHCHLDML.SKLSFKGTF.KFRKIYS.SFPKEFQGCISDFCDPRTL...LWEE
Retrocopy SLPRSQQERSLQEGFIDTHCHLDMLFSKLSFKGTFRKFRKIYSHSFPKEFQGCISDFCDPRTLSNGLWEE

Parental  LLKEDLVWGAFGCHPHFARYYSDVQERNLLQALRHPKAVAFGEMGLDYSHKCTTPVPEQHKVFERQLQLA
          LLK.DLVWG.FGCHPHFA.YY.D.QERNLLQALRHPKAV.FG.MGLDYSHKCT.P.P.QHKVFERQL.LA
Retrocopy LLKDDLVWGGFGCHPHFACYYNDIQERNLLQALRHPKAVVFGKMGLDYSHKCTMPIPQQHKVFERQLKLA

Parental  VSLKKPLVIHCREADEDLLSIMKKFVPSDYKIHRHCFTGSYPVIEPLLEHFPNMSVGFTAVLTYSSAWEA
          VSLKKPLVIHCR.ADEDLLSIMK.FVPSDYKIHRHCFTGSYPVIEPLL..FPNMSVGFTAV.TYSSAWE.
Retrocopy VSLKKPLVIHCRNADEDLLSIMKAFVPSDYKIHRHCFTGSYPVIEPLLKYFPNMSVGFTAVVTYSSAWEV

Parental  REALKQIPLERIIVETDAPYFLPRQVPRSVCQYAHPGLALHTVREIARVKDQPLSHTLATLRENTSRLYN
          R.ALK.IPLERIIVETDAPYFLPR.VP..VCQYAHPGLAL.TVREIA..K...LSHTLATLRENTSRLY.
Retrocopy RNALKKIPLERIIVETDAPYFLPRGVPKRVCQYAHPGLALYTVREIASIKEESLSHTLATLRENTSRLYS

Parental  L
          L
Retrocopy L

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	16.82 RPM
SRP021940_cerebellum	0.00 RPM	27.47 RPM
SRP021940_embryo	0.03 RPM	29.66 RPM
SRP021940_placental_villous	0.00 RPM	17.90 RPM
SRP021940_synovial_membrane	0.00 RPM	24.93 RPM
SRP021940_testis	0.38 RPM	32.10 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1057 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1057 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1057 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016012	1 retrocopy	retro_amel_46,
Canis familiaris	ENSCAFG00000005131	1 retrocopy	retro_cfam_2059,
Equus caballus	ENSECAG00000010589	1 retrocopy	retro_ecab_1057 ,
Mustela putorius furo	ENSMPUG00000017160	1 retrocopy	retro_mputfur_757,