RetrogeneDB ID: retro_cfam_1480

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:32111702..32112959(+)
• Located in intron of: ENSCAFG00000011643

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM22
• Ensembl ID: ENSCAFG00000018082
• Aliases: None
• Description: RNA binding motif protein 22 [Source:HGNC Symbol;Acc:25503]

Sequence

>retro_cfam_1480
ATGGCGACCTCTATGGGTTCCAACACCTACAACAGGCAGAACTGGGAGGATGCGGACTTCCCCATTCTGTGCCAGACGTG
TCTAGGAGAAAACCCATATATCCGAATGACCAAAGAAAAGTATGGGAAAGAATGTAAAATCTGTGCCAGGCCATTCACAG
TGTTTCGCTGGTGCCCCGGGGTCCGCATGCATTTCAAGAAAACTGAAGTGTGCCAAACCTGTAGTAAATTGAAGAATGTC
TGTCAGACCTGCCTTTTGGACCTTGAGTACGGCCTGCCCATCCAGGTTCGTGATGCAGGATTGTCTTTTAAGGATGACAT
GCCAAAGTCAGATGTCAACAAAGAGTACTACACACAGAATATGGAGAGAGAAATTTCTAACTCTGATGGAACGCGACCAG
TTGGCATGTTGGGGAAAGCTACATCCACCAGTAACATGCTGCTCAAGCTGGCCCAGACCACACCCTACTACAAGAGGAAT
CGACCCCACATTTGCTCCTTCTGGGTAAAAGGAGAATGTAAGAGAGGAGAGGAATGTCCATACAGACATGAAAAACCAAC
AGATCCAGATGACCCCCTTGCTGATCAGAACATTAAAGACCAATATTATGGTATCAATGACCCTGTGGCAGATAAGCTTC
TAAAGCGAGCTTCCACAATGCCTCATCTGGACCCGCCAGAGGACAAGACTATCACCACACTATATGTTGGTGGTCTGGGC
GATACTATTACTGAGACTGATCTAAGAAATCACTTCTACCAGTTTGGAGAAATCCGGACGATCACTGTTGTGCAAAGACA
GCAGTGTGCGTTCATCCAGTTTGCCACGAGGCAGGCTGCAGAGGTGGCTGCGGAGAAATCCTTTAATAAGTTGATTGTCA
ATGGCCGTAGACTCAACGTGAAATGGGGAAGGTCCCAAGCAGCCAGAGGAAAAGAAAAAGAGAAGGATGGGACCACAGAC
TCTGGGATCAAGCTAGAGCCCGTTCCGGGACTGCCAGGAGCTCTTCCTCCTCCTCCTGCAGCAGAAGAAGAAACCTCTGC
CAACTACTTCAACCTGCCCCCGAGTGGTCCTCCAGCTGTGAACATTGCACTGCCACCTCCCCCTGGTATTGCCCCACCCC
CACCCCCAGGTTTTGGGCCACACATGTTCCACCCAATGGGACCACCCCCTCCTTTCATGAGGGCTCCAGGACCAATCCAC
TATCCTTCTCAGGACCCTCAGAGGATGGGAGCTCATGCTGGGAAACACAGCAGTCCC

Alignment

ORF - retro_cfam_1480 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.63 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPGVRMRFKKTEV
          MATS.GSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPGVRM.FKKTEV
Retrocopy MATSMGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPGVRMHFKKTEV

Parental  CQTCSKLKNVCQTCLLDLEYGLGLPIQVRDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLG
          CQTCSKLKNVCQTCLLDLEYGL..PIQVRDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLG
Retrocopy CQTCSKLKNVCQTCLLDLEYGL--PIQVRDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLG

Parental  KATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDP
          KATSTS.MLLKLA.TTPYYKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKD.YYGINDP
Retrocopy KATSTSNMLLKLAQTTPYYKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDQYYGINDP

Parental  VADKLLKRASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQ
          VADKLLKRASTMP.LDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQ
Retrocopy VADKLLKRASTMPHLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQ

Parental  AAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKEKEKDGTTDSGIKLEPVPGLPGALPPPPAAEEEASAN
          AAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKEKEKDGTTDSGIKLEPVPGLPGALPPPPAAEEE.SAN
Retrocopy AAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKEKEKDGTTDSGIKLEPVPGLPGALPPPPAAEEETSAN

Parental  YFNLPPSGPPAVVNIALPPPPGIAPPPPPGFGPHMFHPMGPPPPFMRAPGPIHYPSQDPQRMGAHAGKHS
          YFNLPPSGPPA.VNIALPPPPGIAPPPPPGFGPHMFHPMGPPPPFMRAPGPIHYPSQDPQRMGAHAGKHS
Retrocopy YFNLPPSGPPA-VNIALPPPPGIAPPPPPGFGPHMFHPMGPPPPFMRAPGPIHYPSQDPQRMGAHAGKHS

Parental  SP
          SP
Retrocopy SP

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	1.97 RPM	17.81 RPM
SRP017611_brain	1.03 RPM	11.27 RPM
SRP017611_kidney	1.06 RPM	12.68 RPM
SRP017611_liver	1.16 RPM	6.89 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1480 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1480 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1480 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018082	1 retrocopy	retro_cfam_1480 ,
Callithrix jacchus	ENSCJAG00000020963	6 retrocopies	retro_cjac_1338, retro_cjac_2471, retro_cjac_3342, retro_cjac_3390, retro_cjac_3934, retro_cjac_990,
Cavia porcellus	ENSCPOG00000001946	2 retrocopies	retro_cpor_280, retro_cpor_283,
Dasypus novemcinctus	ENSDNOG00000011166	1 retrocopy	retro_dnov_2298,
Homo sapiens	ENSG00000086589	2 retrocopies	retro_hsap_3465, retro_hsap_4273,
Gorilla gorilla	ENSGGOG00000012947	2 retrocopies	retro_ggor_2337, retro_ggor_2859,
Myotis lucifugus	ENSMLUG00000009040	2 retrocopies	retro_mluc_1453, retro_mluc_153,
Macaca mulatta	ENSMMUG00000020683	4 retrocopies	retro_mmul_1199, retro_mmul_1348, retro_mmul_1553, retro_mmul_1762,
Monodelphis domestica	ENSMODG00000009574	1 retrocopy	retro_mdom_186,
Pongo abelii	ENSPPYG00000015955	4 retrocopies	retro_pabe_1412, retro_pabe_1594, retro_pabe_2861, retro_pabe_3486,
Pan troglodytes	ENSPTRG00000017423	2 retrocopies	retro_ptro_2348, retro_ptro_2898,
Tarsius syrichta	ENSTSYG00000003939	3 retrocopies	retro_tsyr_1090, retro_tsyr_1187, retro_tsyr_1231,