RetrogeneDB ID: retro_ecab_807

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:31874048..31875299(-)
• Located in intron of: ENSECAG00000017842

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCP1
• Ensembl ID: ENSECAG00000025146
• Aliases: None
• Description: CUB domain containing protein 1 [Source:HGNC Symbol;Acc:24357]

Sequence

>retro_ecab_807
TGCACGGACCACCGGTACTGCCACAAGAAGTCTTACCCACTCCGGGTGCCCAGCAACATCCTCCAGCTGGCTGTGCAGCT
GCACAGCTTCTCCTGGAAGCTGCTGGTGCCCAAGGACAGTCTCAGCCTGGCACGGGTGCCAGTCCAGAAGCTGCAGCAGC
ACTCACACAAGAGGGCCTGCAACACCAGCTTCAGCTACTTCGTGGCCAGTGCTGTTCCCGGCCAGGACCTTTACTTCTGC
TCCGGAGGCTCCAGTGAGCAGATCCAGGTGAAGCAGAACATCTCGGTGACTCTCCACACCTTTGCCTCCAGCTTCCAACA
GGATGTCTCCAGGCAGGGCCTGACCGTGTCCTTTAGACCGTACTTCACAGAGGAAGCTGTTTTCACTGTGACCCTGGACA
TGAAAAGCAAGGTCTATCTGAGGACCCCTAACTGGGACTGGGGCCTGCTGTCCCTCGCCTCGGTGTCCTGGAACATCAGT
GTGCCCAGAGACCAGGTGGCCTGCCTGACCTTCTTAAAGGAGTGGACTGACCTGGTCTGCCAGACAGGGCGTGCATTCAT
GATCATCCAGGAGCAGCGGATGTGGGCTGAGGAGATCTTTAGCCTGGAGGATGTGCTCCCCAAGCCAAGATTCCACCATC
ATGGTTTCTGGGTCAACATCTCCAATTGCAGCCCTGTGAGCAGCAAGCAGCTGGACATGCTCTTCTGGGTGTCACTTTCC
CTGAGGACAACGGACGTGACTGTTGTCATCATTGCAGTGGTGGGAGGTGGCGCCTTACTGATGTTTGCCCTCGGACTCAT
CATTTGCCTCGTGAAAAAGAAGAGGAAAAAGGAGATAAACAAGGGCCCGGCCGTAGGTATCTACAATGGCAATGTCAATA
CCTAGACGCTGATGCAGCCAAAAAAGTTTCAGAAGAGGTGAAAGGACAATGACTCCCATGTGTATGCAGTCATCGATGAC
ACTATGGTATATGGGCATCTGCTGCAGGATTCCAACAGGTCCTTCCTCCAGCCAGAGGTGGACACCTACCAGCCCTTCCA
GGGCCCCATGGGGGACTGCCCTCCCTCCCCACCCCCCGTATGCTCCAGGGCCCCGACTGTAAAGTTGATCATAGATGAAC
CACCCCCTGACATTCCTCCTGAGTCTGAGAGCAAACCATGCATCTTCTCCCACCCCAACATAGAGAATGTAAGCAACGGG
AACACAGACATTCCCTTGCTGGATGCCCACAAGCCAGTGGAGCCGGGGGAA

Alignment

ORF - retro_ecab_807 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 50.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CTDRRYCHKKSYPLQVPSNILQLPVQLHNFSWKLLVPKDSLSLVLVPVQKLQQHTYERACNTSFRYLVAS
          CTD.RYCHKKSYPL.VPSNILQL.VQLH.FSWKLLVPKDSLSL..VPVQKLQQH...RACNTSF.Y.VAS
Retrocopy CTDHRYCHKKSYPLRVPSNILQLAVQLHSFSWKLLVPKDSLSLARVPVQKLQQHSHKRACNTSFSYFVAS

Parental  AVPSQDLYFGSFCSGGSIEQIQVKQNISVTLRTFSPSYQQDISRQGLTVSFRPYFTEEAVFTVTPDVKSK
          AVP.QDLY...FCSGGS.EQIQVKQNISVTL.TF..S.QQD.SRQGLTVSFRPYFTEEAVFTVT.D.KSK
Retrocopy AVPGQDLY---FCSGGSSEQIQVKQNISVTLHTFASSFQQDVSRQGLTVSFRPYFTEEAVFTVTLDMKSK

Parental  VYLRTPNWDRGLPSLASVSWNISVPRDQVACLTFLKERTGLVCQTGRAFMIIQEQRMRAEEIFSLEEVLP
          VYLRTPNWD.GL.SLASVSWNISVPRDQVACLTFLKE.T.LVCQTGRAFMIIQEQRM.AEEIFSLE.VLP
Retrocopy VYLRTPNWDWGLLSLASVSWNISVPRDQVACLTFLKEWTDLVCQTGRAFMIIQEQRMWAEEIFSLEDVLP

Parental  KPRFHHHSFWVNISNCSPVSGKQLDMLFWVLLSPRTTDMTVIIIAVVGGGALLMFALGLIICLVKKKKKK
          KPRFHHH.FWVNISNCSPVS.KQLDMLFWV.LS.RTTD.TV.IIAVVGGGALLMFALGLIICLVKKK.KK
Retrocopy KPRFHHHGFWVNISNCSPVSSKQLDMLFWVSLSLRTTDVTVVIIAVVGGGALLMFALGLIICLVKKKRKK

Parental  EINKGPAVGIYNGNVNTQMPMQSKKFQKRRKDNDSHVYAVIDDTMVYGHLLQDSNGSFVQPEVDTYRPFQ
          EINKGPAVGIYNGNVNT...MQ.KKFQKR.KDNDSHVYAVIDDTMVYGHLLQDSN.SF.QPEVDTY.PFQ
Retrocopy EINKGPAVGIYNGNVNT*TLMQPKKFQKR*KDNDSHVYAVIDDTMVYGHLLQDSNRSFLQPEVDTYQPFQ

Parental  GPTGDCPPSPPPIGFRAPTAKLTTDEPPPDIPPESESEPYTFSHPNKENVSNGNTDIPLLDAHKPAEPGE
          GP.GDCPPSPPP...RAPT.KL..DEPPPDIPPESES.P..FSHPN.ENVSNGNTDIPLLDAHKP.EPGE
Retrocopy GPMGDCPPSPPPVCSRAPTVKLIIDEPPPDIPPESESKPCIFSHPNIENVSNGNTDIPLLDAHKPVEPGE

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	0.41 RPM
SRP021940_cerebellum	0.00 RPM	1.66 RPM
SRP021940_embryo	0.08 RPM	3.66 RPM
SRP021940_placental_villous	0.05 RPM	23.57 RPM
SRP021940_synovial_membrane	0.00 RPM	1.59 RPM
SRP021940_testis	0.00 RPM	1.21 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_807 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_807 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_807 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000025146	1 retrocopy	retro_ecab_807 ,