RetrogeneDB ID: retro_cfam_645

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:2505644..2506925(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAP1
• Ensembl ID: ENSCAFG00000003012
• Aliases: None
• Description: Adenylyl cyclase-associated protein [Source:UniProtKB/TrEMBL;Acc:E2QZ50]

Sequence

>retro_cfam_645
ATGGCCGACATGCAAAAGCTGGTGGAAAGATTGGAGAGGGCAGTGGGCCGCCTGGAGGCAGTATCCCATGCCTCTGACAT
GCACTGTGGGTATGGAGACAGCGCCCCAAAAGCAGGAGCAGCTCCATATGTGCAAGCCTTTGACTTACCGCTTGCCAGTC
CTGGAGCAGAGTACCTGAAGATCAGTGAAGAGGTTGGAGGAGATGGTGTAGTAACATGCGGAGGTGGTCCACATGGGTCT
GAAGTTGGAGCAAGCTCTCTTGTTTGCAGCCTCTCAGTGCCAGCAGCCAGCAGGCAGTAAGCTTTCTGACTTGTTGGCAC
CCATCTCAGAGCAGATCCAAGAAGTGATAACCTTCCAGAGGATGAACAGAAGCAGCAAGTTGTTCAATCACCTGTCAGCT
GTCAGCGATAGTATCCAGGCCCTGGGTTGGGTGACTGTGGCTCCCAAGCCTGGTCCCTGTGTGAAAGAAAGGAACAATGT
TGCCATGTTTTATACAGATTGAGTCCTCAAGGAGACAGATGTTGATAAGAAGCACGGGGACTGGGTCAAAGCTTACTTGA
GTATATGGACTGAGCTACAGGCTTACATTGAGTTCTATACCACTGGACTGGCCTAGACCAAAACAGAGTCTGTGGCAGAA
CTTGGTGGATTGCCATCTGGACCCTCTGCTGGATTAGGTCCTCTTCCTCCCTCCAGCAGCGCCCCCGCACCCCACAGCCA
CCTGTTCAGGCTCAGATGGGCCTGCTTCCCAGCACTGTTGCATAAATTAACCAGGGGAAGAGCATCACACATGCCCTGAA
ACATGTATCTGATGACGTGAAGACTCACAAGAACCCCGCCCTGAAGGCCCAGAGTGGTCCAGTACGAAGCGACCCCAAGC
CATTCTCTGCACCTAAACCAGGAGTCAGCCCATCCCCTAAGCCAACCACTCAGAAGGATCTGGCTGTACCTGAACTGGAG
GGCAAGAAGTGGAGAGTGAGAAATCGGGAGCATGTTTCTAACCTAGTGATTGATGATGACACAGAGCTGAAACAGGTGGC
TTACATATCCAAGTGTGTCAACATGACATTGCAAATCAAGGACAAAATTAAGTCAATTACAGTAGGTAACTGTAAGAAAC
TCGGTCTGGTGTTCAATGATATGGTGGGCATCATGAAGGTAACCAATTGCAGGGATGTCAAAGTTCAAGTAGTGGGTAAA
GTGCCAACGATTTCCATCAGCAAAACAGATGGCTGACACGTTTACCTGAGCAAGAATTCCCTGGATTGCAAGATAGTGTC
A

Alignment

ORF - retro_cfam_645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.7 %
• Parental protein coverage: 90.74 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADMQKLVERLERAVGRLEAVSHASDMHCGYGDSAPKAGAAPYVQAFDSLLAGPVAEYLKISKEIGGD-V
          MADMQKLVERLERAVGRLEAVSHASDMHCGYGDSAPKAGAAPYVQAFD..LA.P.AEYLKIS.E.GGD.V
Retrocopy MADMQKLVERLERAVGRLEAVSHASDMHCGYGDSAPKAGAAPYVQAFDLPLASPGAEYLKISEEVGGD>V

Parental  QKHAEMVHTGLKLERALLVTASQCQQPAGNKLSDLLAPISEQIQEVITYREKNRGSKLFNHLSAVSESIQ
          ..HAE.VH.GLKLE.ALL..ASQCQQPAG.KLSDLLAPISEQIQEVIT....NR.SKLFNHLSAVS.SIQ
Retrocopy **HAEVVHMGLKLEQALLFAASQCQQPAGSKLSDLLAPISEQIQEVITFQRMNRSSKLFNHLSAVSDSIQ

Parental  ALGWVAMAPKPGPYVKEMNDAAMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQAYIKEFHTTGLAWSK
          ALGWV..APKPGP.VKE.N..AMFYT..VLKE..DVDKKH.DWVKAYLSIWTELQAYI.EF.TTGLA..K
Retrocopy ALGWVTVAPKPGPCVKERNNVAMFYTD*VLKE-TDVDKKHGDWVKAYLSIWTELQAYI-EFYTTGLA*TK

Parental  TGPVAQELSGLPSGPSAGSGPPPPPPG-PPPPPVPTSSGSDESASRS-ALFAQINQGESITHALKHVSDD
          T..VA.EL.GL...PS..S....P.P..P..PP.PT...S......S....A.INQG.SITHALKHVSDD
Retrocopy TESVA-ELGGL---PSGPSAGLGPLPP>PAAPPHPTATCSGSDGPAS>STVA*INQGKSITHALKHVSDD

Parental  MKTHKNPALKAQSGPVRSGPKPFSAPKPGVSPSPKPTAKKEPAVLELEGKKWRVENQENVSNLVI-DDTE
          .KTHKNPALKAQSGPVRS.PKPFSAPKPGVSPSPKPT..K..AV.ELEGKKWRV.N.E.VSNLVI.DDTE
Retrocopy VKTHKNPALKAQSGPVRSDPKPFSAPKPGVSPSPKPTTQKDLAVPELEGKKWRVRNREHVSNLVIDDDTE

Parental  LKQVAYIYKCVNTTLQIKGKINSITVDNCKKLGLVFDDVVGIVEIINSRDVKVQVMGKVPTISINKTDGC
          LKQVAYI.KCVN.TLQIK.KI.SITV.NCKKLGLVF.D.VGI....N.RDVKVQV.GKVPTISI.KTDG.
Retrocopy LKQVAYISKCVNMTLQIKDKIKSITVGNCKKLGLVFNDMVGIMKVTNCRDVKVQVVGKVPTISISKTDG*

Parental  HVYLSKNSLDCEIVS
          HVYLSKNSLDC.IVS
Retrocopy HVYLSKNSLDCKIVS

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
SRP012049_cerebellum	0.13 RPM	93.36 RPM
SRP017611_brain	0.32 RPM	163.39 RPM
SRP017611_kidney	0.13 RPM	79.44 RPM
SRP017611_liver	0.15 RPM	37.20 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_645 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_645 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_645 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 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 ,
Canis familiaris	ENSCAFG00000009977	1 retrocopy	retro_cfam_1385,
Equus caballus	ENSECAG00000024658	1 retrocopy	retro_ecab_119,
Homo sapiens	ENSG00000131236	2 retrocopies	retro_hsap_2666, retro_hsap_664,
Gorilla gorilla	ENSGGOG00000027527	2 retrocopies	retro_ggor_1860, retro_ggor_575,
Macropus eugenii	ENSMEUG00000004960	1 retrocopy	retro_meug_544,
Myotis lucifugus	ENSMLUG00000011626	1 retrocopy	retro_mluc_847,
Mus musculus	ENSMUSG00000028656	1 retrocopy	retro_mmus_1265,
Nomascus leucogenys	ENSNLEG00000012077	2 retrocopies	retro_nleu_1600, retro_nleu_2221,
Otolemur garnettii	ENSOGAG00000005492	1 retrocopy	retro_ogar_299,
Pongo abelii	ENSPPYG00000001496	4 retrocopies	retro_pabe_2212, retro_pabe_2358, retro_pabe_2415, retro_pabe_584,
Pan troglodytes	ENSPTRG00000000583	2 retrocopies	retro_ptro_1796, retro_ptro_484,
Rattus norvegicus	ENSRNOG00000013492	1 retrocopy	retro_rnor_1180,
Tursiops truncatus	ENSTTRG00000004358	1 retrocopy	retro_ttru_1689,