RetrogeneDB ID: retro_ecab_119

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:33455050..33456474(+)
• Located in intron of: ENSECAG00000016847

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAP1
• Ensembl ID: ENSECAG00000024658
• Aliases: None
• Description: CAP, adenylate cyclase-associated protein 1 (yeast) [Source:HGNC Symbol;Acc:20040]

Sequence

>retro_ecab_119
ATGGCTGACATGCAAAATCTGGTAGAAAGATTAGAGAGGGCGGTGGGCCGCCTGGAGGCAGTATCTCAGTCCTCTGGCAT
GCACTATGGACATGGAGACAGTGCCCCAAAAGCAGGAACAGCTCCATATGTGCAAGTATTTGACTCACTGCTGGCCGGTC
CTATGGCAGAGTACCTGAAGATCAGTAAAGAGATTGGGGGAGATGTGGAGAAACATGCGGAGATGGTCCACACAGGTCTG
AAGTTGGAGCGAGCTCTCTTGGTTACAGCCTCTCAGTGCCAGCAGCCTGCAGGCAATAAGCTTTCTGATTTGTTGGCACC
CATCTCAGAGCAGATCCAAGAAGTGATAACGTTTCCAGAGAAGAACCAAGGCAGCAAGTTGTTCAATCACCTGTCGGCCG
TCAGCGAAAGTATCCAGGCCCTGGGTTGCGTGGCTGTGGCTCCCAAGCCTGGTCCCTATGTGAAAGAAATGAATGATGCT
GCCATGTTTTATACAAACCGAGTCCTGAAGGAGTACAAAGATGTGGATAAGAAGCATGTGGACTGGGTCAAAGCTTACTT
GAGTATATGGACAGAGCTGCAGGCTTACATTAAACAGTTCCATACCACCAGACTGGCCTGGAGCAAAACGGGACCTGTGG
CAAAAAAACTGACTGGACTGCCATCTGGACCCTCTGCTGGATCCGGTCCTCCTCCCCCGCCACCAGGCCCACCTCCTCCC
CCAGTCCCCACCAGTTCAGGCTCTGATGAGTCTGCTTCACGCTCTGCCCTGTTTGCTCAGATTAATCAGGGGGAGAGCAT
CACACATGCCCTGAAACATGTATCTGATGACATGAAGACGCACAAGAACCCCGCCCTGAAGGCTCAGAGTGGGCCAGTGC
GAAGTGGCCCCAAACCATTCTCTGCACCTAAACCAGGAGGCAGCCCATCCCCCAAACCAGCCACAAAGAAGGAGCCACCT
CTACTTGAACTGGAGGGCAAAAAGTGGAGAGTGGAAAATCAGGAGAATGTTTCCAACCTGGTAATTGATGACACGGAGCT
GAAATAGGTGGCTTACATATACAAGTGTGTCAACACAACATTGCAAATCGAGGGCAAAATTAACTCCATTACAGTAGATA
ACTGTAAGAAACTCGGCCTGGTGTTCGATGACGTGGTGGGCATAGTGGAGATAATCAATAGTAGGGATGTCAAAGTTCAG
GTAATGGGTAAAGTGCCAACCATTTCCATCAACAAAACAGATGGCTGCCACGTTTCCCTAGCAAGAATTCCCTGGATTGT
GAGATAGTCAGTGCCAAATCTTCTGAAATGAATGTCCTCATTCCTACAGAAGGCGGTGACTTTAATGAGTTCCCAGTCCC
TGAGCAGTTCAAGACCCTATGGAATGGGCAGAAGTTGGTCACCACAGTGACAGAAATTGCCGGA

Alignment

ORF - retro_ecab_119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADMQNLVERLERAVGRLEAVSQSSDMHCGHGDSAPKAGTAPYVQVFDSLLAGPVAEYLKISKEIGGDVQ
          MADMQNLVERLERAVGRLEAVSQSS.MH.GHGDSAPKAGTAPYVQVFDSLLAGP.AEYLKISKEIGGDV.
Retrocopy MADMQNLVERLERAVGRLEAVSQSSGMHYGHGDSAPKAGTAPYVQVFDSLLAGPMAEYLKISKEIGGDVE

Parental  KHAEMVHTGLKLERALLVTASQCQQPAGNKLSDLLAPISEQIQEVITFREKNRGSKLFNHLSAVSESIQA
          KHAEMVHTGLKLERALLVTASQCQQPAGNKLSDLLAPISEQIQEVITF.EKN.GSKLFNHLSAVSESIQA
Retrocopy KHAEMVHTGLKLERALLVTASQCQQPAGNKLSDLLAPISEQIQEVITFPEKNQGSKLFNHLSAVSESIQA

Parental  LGWVAMAPKPGPYVKEMNDAAMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQAYIKEFHTTGLAWSKT
          LG.VA.APKPGPYVKEMNDAAMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQAYIK.FHTT.LAWSKT
Retrocopy LGCVAVAPKPGPYVKEMNDAAMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQAYIKQFHTTRLAWSKT

Parental  GPVAKELSGLPSGPSAGSGPPPPPPGPPPPPVPTSSGSDESASRSALFAQINQGESITHALKHVSDDMKT
          GPVAK.L.GLPSGPSAGSGPPPPPPGPPPPPVPTSSGSDESASRSALFAQINQGESITHALKHVSDDMKT
Retrocopy GPVAKKLTGLPSGPSAGSGPPPPPPGPPPPPVPTSSGSDESASRSALFAQINQGESITHALKHVSDDMKT

Parental  HKNPALKAQSGPVRSGPKPFSAPKPGGSPSPKPATKKEPPLLELEGKKWRVENQENVSNLVIDDTELKQV
          HKNPALKAQSGPVRSGPKPFSAPKPGGSPSPKPATKKEPPLLELEGKKWRVENQENVSNLVIDDTELK.V
Retrocopy HKNPALKAQSGPVRSGPKPFSAPKPGGSPSPKPATKKEPPLLELEGKKWRVENQENVSNLVIDDTELK*V

Parental  AYIYKCVNTTLQIKGKINSITVDNCKKLGLVFDDVVGIVEIINSRDVKVQVMGKVPTISINKTDGCHVYL
          AYIYKCVNTTLQI.GKINSITVDNCKKLGLVFDDVVGIVEIINSRDVKVQVMGKVPTISINKTDGCHV.L
Retrocopy AYIYKCVNTTLQIEGKINSITVDNCKKLGLVFDDVVGIVEIINSRDVKVQVMGKVPTISINKTDGCHVSL

Parental  -SKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFKTLWNGQKLVTTVTEIAG
          .SKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFKTLWNGQKLVTTVTEIAG
Retrocopy <SKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFKTLWNGQKLVTTVTEIAG

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	0.30 RPM	23.67 RPM
SRP021940_cerebellum	0.99 RPM	62.53 RPM
SRP021940_embryo	1.61 RPM	66.72 RPM
SRP021940_placental_villous	1.54 RPM	156.31 RPM
SRP021940_synovial_membrane	1.32 RPM	89.60 RPM
SRP021940_testis	1.09 RPM	126.67 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_119 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_119 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_119 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004417	1 retrocopy	retro_amel_1891,
Bos taurus	ENSBTAG00000013363	1 retrocopy	retro_btau_460,
Canis familiaris	ENSCAFG00000003012	2 retrocopies	retro_cfam_1316, retro_cfam_645,
Equus caballus	ENSECAG00000024658	1 retrocopy	retro_ecab_119 ,
Macropus eugenii	ENSMEUG00000004960	1 retrocopy	retro_meug_544,
Tursiops truncatus	ENSTTRG00000004358	1 retrocopy	retro_ttru_1689,