RetrogeneDB ID: retro_cfam_560

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:4087313..4088569(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000000632
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000012160
• Aliases: None
• Description: None

Sequence

>retro_cfam_560
CCGCCCACTAGTTATCCCCCCCAAACTGGATCCTACAGCCAGGCGCCAAGTCAATATAGCCAACAGAGCAGCAGCTACGG
GCAGCAGAGTTCATTCAGACAGGACCACCCCAGTAGCATGGGTGTTTATGGGCAGGAGTCTGGAGGATTTTCCGGACCAG
GAGAGAACCGGAGCATGAGTGGCCCTGATAACCGGGGCAGGGGAAGAGGGGGATTTGATCGTGGAGGCATGAGCAGAGGT
GGGCGGGGAGGAGGACGCGGTGGAATGGGTGCTGGAGAGCGAGGTGGCTTCAATAAGCCTGGTGGACCCATGGATGAAGG
ACCAGATCTTGATCTAGGCCCACCTGTAGATCCAGATGAAGACTCTGACAACAGTGCAATTTATGTGCAAGGCCTAAATG
ACAATGTGACTCTAGATGATCTTGCTGACTTTAAGCAATGTGGAGTTGTTAAGATGACAAGAGAACCGGACAACCCATGA
TCCATATCTACTTGGACAAGGAAACAGGAAAGCCCAAAGGTGATGCTACAGTATCCTATGAAGACCCACCAACTGCCAAG
GCTGCTGTGGAGTGGTTTGAAGGAAAAGATTTTCAAGGAAGCAAACTTAAGGTTTCTCTTGTTCGGAAGAAACCTCCAAT
GAACAGCATGCGGGGTGGTATGCCTCCCCGTGAGGGCAGAGGGATGCCACCACCACTCCGTGGAGGTCCAGGGGGCCCAG
GAGGTCCTGGGGGCCCCATAGGTCGCATGGGAGGCAGTGGAGGAGACAGAGGTGGCTTTCCCCCAAGAGGACCCCGGGGT
TCCCGAGGGAACCCATCTGGAGGAGGAAACGTCCAGCACCGAGCTGGGGACTGGCAGTGCCCCAATCCGGGGTGTGGAAA
CCAGAACTTCGCCTGGAGAACAGAATGCAACCAGTGTAAGGCCCCAAAGCCTGAAGGCTTCCTTCCACCACCCTTCGCGC
CCCCGGGGGGTGACCGTGGCAGAGGCGGCCCTGGTGGCATGCGGGGAGGACGAGGTGGCCTCATGGACCGCGGTGGTCCC
GGTGGGATGTTCAGAGGTGGCCGCGGTGGAGACAGAGGGGGCTTCCGTGGTGGCCGGGGCATGGACCGAGGTGGCTTTGG
CGGAGGAAGACGAGGCGGTCCTGGTGGGCCCCCTGGACCTTTGATGGAACAGATGGGAGGAAGAAGAGGCGGGCGTGGAG
GACCTGGAAAACTGGATAAAGGCGAGCACCGTCAGGAGCGCAGAGACCGGCCCTAC

Alignment

ORF - retro_cfam_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.39 %
• Parental protein coverage: 62.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPTSYPPQTGSYSQAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQESGGFSGPGENRSMSGPDNRGRGRG
          PPTSYPPQTGSYSQAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQESGGFSGPGENRSMSGPDNRGRGRG
Retrocopy PPTSYPPQTGSYSQAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQESGGFSGPGENRSMSGPDNRGRGRG

Parental  GFDRGGMSRGGRGGGRGGMGSAGERGGFNKPGGPMDEGPDLDKGPPVDPDEDSDNSAIYVQGLNDNVTLD
          GFDRGGMSRGGRGGGRGGMG.AGERGGFNKPGGPMDEGPDLD.GPPVDPDEDSDNSAIYVQGLNDNVTLD
Retrocopy GFDRGGMSRGGRGGGRGGMG-AGERGGFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAIYVQGLNDNVTLD

Parental  DLADFFKQCGVVKM-NKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSL
          DLADF.KQCGVVKM..KRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWF.GKDFQGSKLKVSL
Retrocopy DLADF-KQCGVVKM<DKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFEGKDFQGSKLKVSL

Parental  ARKKPPMNSMRGGMPPREGRGMPPPLRGGPGGPGGPGGPMGRMGGRGGDRGGFPPRGPRGSRGNPSGGGN
          .RKKPPMNSMRGGMPPREGRGMPPPLRGGPGGPGGPGGP.GRMGG.GGDRGGFPPRGPRGSRGNPSGGGN
Retrocopy VRKKPPMNSMRGGMPPREGRGMPPPLRGGPGGPGGPGGPIGRMGGSGGDRGGFPPRGPRGSRGNPSGGGN

Parental  VQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPPPGGDRGRGGPGGMRGGRGGLMDRGGP
          VQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPF.PPGGDRGRGGPGGMRGGRGGLMDRGGP
Retrocopy VQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFAPPGGDRGRGGPGGMRGGRGGLMDRGGP

Parental  GGMFRGGRGGDRGGFRGGRGMDRGGFGGGRRGGPGGPPGPLMEQMGGRRGGRGGPGKMDKGEHRQERRDR
          GGMFRGGRGGDRGGFRGGRGMDRGGFGGGRRGGPGGPPGPLMEQMGGRRGGRGGPGK.DKGEHRQERRDR
Retrocopy GGMFRGGRGGDRGGFRGGRGMDRGGFGGGRRGGPGGPPGPLMEQMGGRRGGRGGPGKLDKGEHRQERRDR

Parental  PY
          PY
Retrocopy PY

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	1.68 RPM	77.74 RPM
SRP017611_brain	0.16 RPM	36.04 RPM
SRP017611_kidney	0.46 RPM	45.24 RPM
SRP017611_liver	0.22 RPM	33.94 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_560 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_560 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008298	2 retrocopies	retro_amel_191, retro_amel_959,
Canis familiaris	ENSCAFG00000012160	8 retrocopies	retro_cfam_1142, retro_cfam_1183, retro_cfam_1225, retro_cfam_133, retro_cfam_1397, retro_cfam_1736, retro_cfam_1889, retro_cfam_560 ,
Callithrix jacchus	ENSCJAG00000019987	4 retrocopies	retro_cjac_1716, retro_cjac_2022, retro_cjac_2813, retro_cjac_2911,
Cavia porcellus	ENSCPOG00000009502	1 retrocopy	retro_cpor_1353,
Felis catus	ENSFCAG00000004243	1 retrocopy	retro_fcat_519,
Homo sapiens	ENSG00000182944	1 retrocopy	retro_hsap_463,
Gorilla gorilla	ENSGGOG00000012212	1 retrocopy	retro_ggor_444,
Macropus eugenii	ENSMEUG00000008703	1 retrocopy	retro_meug_1424,
Myotis lucifugus	ENSMLUG00000012058	1 retrocopy	retro_mluc_328,
Monodelphis domestica	ENSMODG00000008679	1 retrocopy	retro_mdom_279,
Mustela putorius furo	ENSMPUG00000013432	2 retrocopies	retro_mputfur_56, retro_mputfur_572,
Mus musculus	ENSMUSG00000009079	1 retrocopy	retro_mmus_1379,
Oryctolagus cuniculus	ENSOCUG00000004432	2 retrocopies	retro_ocun_1346, retro_ocun_242,
Pongo abelii	ENSPPYG00000011684	1 retrocopy	retro_pabe_1769,
Pan troglodytes	ENSPTRG00000014218	1 retrocopy	retro_ptro_350,
Ictidomys tridecemlineatus	ENSSTOG00000023177	1 retrocopy	retro_itri_1892,
Tursiops truncatus	ENSTTRG00000011881	1 retrocopy	retro_ttru_1366,