RetrogeneDB ID: retro_btau_460

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:15274613..15276026(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000045689
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CAP1
• Ensembl ID: ENSBTAG00000013363
• Aliases: None
• Description: Adenylyl cyclase-associated protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3SYV4]

Sequence

>retro_btau_460
ATGGCTGACATGCGAAATCTGGTAGAAAGATTGGAGAGAGTGGTGGGCCGCCTGGAGGCAGTCTCCCATGCCTCTGACAC
ACACTGTGGGTATGGAGACAGTGCTGCAAAAGGAACGACTCCATATGTGCAAGCATTTGACTCACTGCTGGCCGGTCCTG
TGGCAGAGTACCTCAAGATCAGTAAAGAGAGTGGGGGAGATGTGCAGAAACATGCGGAGATGGTCCACACAGGTCTGAAG
TTAGAGCGAGCTCTCTTGGTTACAGCCTCTCAGTGCCAGCAGCCAGCAGGCAACAAACTTTCTGACTTGTTGGCACCCAT
CTCCGAGCAGATCCAAGAAGTGGTGACCTTCCGGGAGAAGAACCGAGGCAGCAAGTTGTTCAATCACCTGTCAGCTGTCA
GCGAAAGTATCCAGGCCCTGGGTTGGGTGGCTATGGCTCCCAAGCCTGGTCTCTATGTGAAGGAAATGAATGATGCTGCC
ATGTTTTATACAAATCGAGTCCTCAAGGAGTACAAAGATGTGGATAAAAAGCATGTGGACTGGGTCAAAGCTTACTTGAG
TATATGGACAGAGCTGCAGGCTTACATTAAGGAGTTCCATACCACCGGACTGGCCTGGAGCAGAACGGGGCCTGTGGCAA
AAGAACTGAGTGGCTTGCCATCTGGACCCTCTGCTGGATCTGGTCCTCCTCCTCCCCCCCGCCAGGTCCACCTCCCCCCG
CCAGTCCCCACCAGTTCAGGCTCAGATGACTCTGCTTCACGCTCAGCACTGTTTGCGCAGATTAATCAGGGGGAGAGCAT
CATACATGCCCTGAAACACGTATCTGATGACATGAAGACTCACAAGAACCCTGCCTTGAAGGCTCAGAGTGGTCTGATAC
GAAGTGGCCCCAAACCCTTCTCTGCATCTAAACCAGATCCCCCCAAACCAGTCACAAAGAAGGAACCAGCCCTACTTGAA
CTGGAGGGCAAGAAGTGGAGAGTGGAAAATCAGGAGAATGTTTCCAACCTGGTGATAGAGGATACAGAGCTGAAACAGGT
GGCTTACATATTCAAGTGTGTGAACTCGACATTGCAGATCAAGGGCAAAATTAACTCCATTACTGTAGATAACTGTAAGA
AACTTGGTCTGGTGTTTGATGACGTGGTGGGCATTGTGGAGATAATCAATAGTAAGGATGTCACAGTTCAGGTAATGGGT
AAAGTGCCAACCATTTCCATCAACAAAACAGATGGCTGCCACGTTTACCTGAGCAAGAACTCCCTGGATTGTGAGATAGT
CAGTGCCAAATCTTCTGAGATGAATGTCATTCCTACAGAAGGCGGTGACTTCAATGAGTTCCCAGTCGCTGAGCAGTTTA
AGACCCTATGGAATGGGCAGAAGTTGGTCACCACAGTGACAGAAATTGCTGGA

Alignment

ORF - retro_btau_460 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADMRNLVERLERVVGRLEAVSHASDTHCGYGDSAAKGTTPYVQAFDSLLAGPVAEYLKISKEIGGDVQK
          MADMRNLVERLERVVGRLEAVSHASDTHCGYGDSAAKGTTPYVQAFDSLLAGPVAEYLKISKE.GGDVQK
Retrocopy MADMRNLVERLERVVGRLEAVSHASDTHCGYGDSAAKGTTPYVQAFDSLLAGPVAEYLKISKESGGDVQK

Parental  HAEMVHTGLKLERALLVTASQCQQPAGNKLSDLLAPISEQIQEVVTFREKNRGSKLFNHLSAVSESIQAL
          HAEMVHTGLKLERALLVTASQCQQPAGNKLSDLLAPISEQIQEVVTFREKNRGSKLFNHLSAVSESIQAL
Retrocopy HAEMVHTGLKLERALLVTASQCQQPAGNKLSDLLAPISEQIQEVVTFREKNRGSKLFNHLSAVSESIQAL

Parental  GWVAMAPKPGPYVKEMNDAAMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQAYIKEFHTTGLAWSRTG
          GWVAMAPKPG.YVKEMNDAAMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQAYIKEFHTTGLAWSRTG
Retrocopy GWVAMAPKPGLYVKEMNDAAMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQAYIKEFHTTGLAWSRTG

Parental  PVAKELSGLPSGPSAGSGPPPPPPGPPPPPVPTSSGSDD-SASRSALFAQINQGESITHALKHVSDDMKT
          PVAKELSGLPSGPSAGS.................S...D.SASRSALFAQINQGESI.HALKHVSDDMKT
Retrocopy PVAKELSGLPSGPSAGSXXXXXXXXXXXXXXXXTSSGSDDSASRSALFAQINQGESIIHALKHVSDDMKT

Parental  HKNPALKAQSGLIRSGPKPFSASKPDPPKPVAKKEPALLELEGKKWRVENQENVSNLMIEDTELKQVAYI
          HKNPALKAQSGLIRSGPKPFSASKPDPPKPV.KKEPALLELEGKKWRVENQENVSNL.IEDTELKQVAYI
Retrocopy HKNPALKAQSGLIRSGPKPFSASKPDPPKPVTKKEPALLELEGKKWRVENQENVSNLVIEDTELKQVAYI

Parental  FKCVNSTLQIKGKINSITVDNCKKLGLVFDDVVGIVEIINSKDVKVQVMGKVPTISINKTDGCHVYLSKN
          FKCVNSTLQIKGKINSITVDNCKKLGLVFDDVVGIVEIINSKDV.VQVMGKVPTISINKTDGCHVYLSKN
Retrocopy FKCVNSTLQIKGKINSITVDNCKKLGLVFDDVVGIVEIINSKDVTVQVMGKVPTISINKTDGCHVYLSKN

Parental  SLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFKTLWNGQKLVTTVTEIAG
          SLDCEIVSAKSSEMNV.IPTEGGDFNEFPV.EQFKTLWNGQKLVTTVTEIAG
Retrocopy SLDCEIVSAKSSEMNV-IPTEGGDFNEFPVAEQFKTLWNGQKLVTTVTEIAG

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
ERP005899_liver	0.07 RPM	76.78 RPM
ERP005899_muscle	0.90 RPM	313.62 RPM
SRP017611_brain	0.37 RPM	153.39 RPM
SRP017611_kidney	3.85 RPM	211.54 RPM
SRP017611_liver	0.08 RPM	71.58 RPM
SRP030211_testis	0.60 RPM	164.92 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_460 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_460 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_460 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,