RetrogeneDB ID: retro_cfam_1723

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:20881560..20882310(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000013908
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000005777
• Aliases: None
• Description: None

Sequence

>retro_cfam_1723
ATGGGCCACCTGGTGACAACGCAGATGCTGTTCCTTCTGGTGGGGGTGGCCGCAGTACGGACAGCATGGCCCAGAACTGA
GCTTCTCAATGTCTGTATGGACACAAAGCACCACAAGGAAAAGCCAAGCCCAGAGGACGAGCTGCATAAGCAGTGCAGCC
CCTGGAAGAAGAATTCCTGCTGCTTCACCAACACCAGCCAGGAAGCCCATAAGGATATTTCCTACCTGTACAGATTCAAC
TGGAACCATTGCAAATCAATGCCTGCAAAAAGGACTTCATCCAGGACACCTGCCTATATGAGTGTTCCCCCAACCTGGGG
CTCTGGATTCAGAAGGTGAACCCAGGGCTGGCACAAGGAGCACATCCTGCACATAACCCTGTGCAGAGAGGACTGCAAGC
AATGGTGGCAGGACTGCCGCACCTCCTACACCAGCAAGAGCAACTGGCAAAAGGGCTGGAACTGGACCTCAGGGTATAAC
CAGTGTCCAGAGAGAGCTGCCTGCCATCCCTTCCATTTCTACTTCCCCACATCTACTGCTCTGTGCAGTGAAATCTGGAG
TCACTCCTACAAAGTCAGCAACTACAGCTGAGGGAGTGGCCGCTGCATCCAGATGTGGTTCGACCTGGCCCAGGGCAACC
CCAACGAGGAAGTGGTGAGGTTCTATGCTGGGGCCATGAGTGAGGCTGGGCACTGTGTGCTTGGGCCTCTCCTGCTCCGC
CTGGCCCTGATGCTGCTCTAGCTACTTAGC

Alignment

ORF - retro_cfam_1723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQLVTTQVLFLLVGVAAVWTARPRTELLNVCMDAKHHKEKPSPEDGLHKQCSPWKKNSCCFANTSREAH
          M..LVTTQ.LFLLVGVAAV.TA.PRTELLNVCMD.KHHKEKPSPED.LHKQCSPWKKNSCCF.NTS.EAH
Retrocopy MGHLVTTQMLFLLVGVAAVRTAWPRTELLNVCMDTKHHKEKPSPEDELHKQCSPWKKNSCCFTNTSQEAH

Parental  KDISYLYRFNWNHCGSMTPACKKHFIQDTCLYECSPNLGPWIQEVNQSWRKERILHVPLCKEDCEQWWQD
          KDISYLYRFNWNHC.SM.PA.K.............P..G.......Q.W.KE.ILH..LC.EDC.QWWQD
Retrocopy KDISYLYRFNWNHCKSM-PA-KRTSSRTPAYMSVPPTWGSGFRR*TQGWHKEHILHITLCREDCKQWWQD

Parental  CRTSYTCKSNWHKGWNWTSGYNQCPEGAACHPFHFYFPTSAALCSEIWSHSYKVSNYSRGSGRCIQMWFD
          CRTSYT.KSNW.KGWNWTSGYNQCPE.AACHPFHFYFPTS.ALCSEIWSHSYKVSNYS.GSGRCIQMWFD
Retrocopy CRTSYTSKSNWQKGWNWTSGYNQCPERAACHPFHFYFPTSTALCSEIWSHSYKVSNYS*GSGRCIQMWFD

Parental  PAQGNPNEEVARFYARAMSEATHCVLGPPLLSLALMLLWLLS
          .AQGNPNEEV.RFYA.AMSEA.HCVLGP.LL.LALMLL.LLS
Retrocopy LAQGNPNEEVVRFYAGAMSEAGHCVLGPLLLRLALMLL*LLS

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	0.04 RPM	0.00 RPM
SRP017611_brain	0.16 RPM	0.32 RPM
SRP017611_kidney	0.26 RPM	219.71 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1723 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1723 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1723 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005777	1 retrocopy	retro_cfam_1723 ,
Callithrix jacchus	ENSCJAG00000015224	1 retrocopy	retro_cjac_3330,
Dasypus novemcinctus	ENSDNOG00000000856	1 retrocopy	retro_dnov_1751,
Echinops telfairi	ENSETEG00000015365	2 retrocopies	retro_etel_1160, retro_etel_128,
Myotis lucifugus	ENSMLUG00000014126	2 retrocopies	retro_mluc_1199, retro_mluc_567,
Monodelphis domestica	ENSMODG00000008017	1 retrocopy	retro_mdom_990,
Monodelphis domestica	ENSMODG00000008032	1 retrocopy	retro_mdom_588,
Monodelphis domestica	ENSMODG00000008042	1 retrocopy	retro_mdom_648,
Mus musculus	ENSMUSG00000001827	1 retrocopy	retro_mmus_1438,
Oryctolagus cuniculus	ENSOCUG00000000165	1 retrocopy	retro_ocun_472,
Otolemur garnettii	ENSOGAG00000000641	5 retrocopies	retro_ogar_2539, retro_ogar_2666, retro_ogar_2758, retro_ogar_2908, retro_ogar_532,
Tarsius syrichta	ENSTSYG00000003503	3 retrocopies	retro_tsyr_1057, retro_tsyr_111, retro_tsyr_1651,