RetrogeneDB ID: retro_cfam_133

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:66087101..66089054(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000017391
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_cfam_133
ATGGCGTCCACGGATTACAGTACCTACAGCCAAGCTGCAGCCCAGCAGGGCTACAGTGGATACACCGCCCAACCAACTCA
AGGATATGCACAGACCACCCAGGCATATGGGCATCAGAGTTATGGAACCTATGGACAGCCCACTGACGTCAGCTATACCC
AGGCTCAGACCACTGCGACTTATGGGCAGACCGCCTATGCAACTTCTTATGGACAGCCTCCCGCTGGTTATACTACTCCA
ACTGCCCCTCAGGCATACATTCAGCCTGTCCAGGGGTACGGCGCTGGTGCTTATGATACCACCACTGCTATGGTCACTAC
CACCCAGGCCTCCTATGCTGCTCAGTCTACATATGGCACTCAGCCTGCTTACCCAGCCTATGGGCAGCAGCCAGCGGCCA
CCGCACCTGCAAGACCACAGGAAGGTAACAAACCTGCTGAGACTAGTCAACCTCAATCTAGCATAGGGGGTTACAACCAG
CCCAGCCTAGGATATGGACAGAGTAACTACAGTTATCCCCAGGTACCTGGGAGCTACCCCATGCAGCCAGTCACAGCACC
ACCATCTTATCCTCCTACCAGCTACTCCTCTACACAGCCGACTAGTTATGATCAGAGCAGTTACTCTCAACAGAACACCT
ATGGGCAGCCGAGCAGCTATGGACAGCAGAGTAGCTATGGTCAACAAAGCAGCTATGGGCAGCAGCCGCCCACTAGTTAT
CCCCCTCAAACTGGATACTACAGCCAGGCTCCAAGTCAATATAGCCAACAGAGCAGCAGCTACGGGCAGCAGAGTTCATT
CCAACAGGACCACCCCAGTAAGATGGGTGTTTATGGGCAGGAGTCTGGAGGATTTTCCGGACCAGGAGAGAACCAGAGCA
TGAGTGGCACTGATAACCGGGGCAGGGGAAGAGGGGGATTTGATCATGCAGGCATGAGCAGAGGTGGACGGGGAGGAGGA
CGCGGTGGAATGGGCAGCGCTGGAGAGCGAGGTGGCTTCAATAAGCCTGGTGGACCCATGGATGAAGGACCAGATCTTGA
TCTAGGCCCACCTGTAGATCCAGATGAAGACTCTGACAACAATGCAATTTACGTGCAAGGCTTAAATGACAATGTGACTC
TAGATGATGTGGCTGACTTATTTAAGCAGTGTGGAATTGTTAAGATGAACAAGAGAACCGGACAACCCATGATCCATATC
TACTTGGATAAGGAAACAGGAAAGCCCAAAGGTGATGCTACAGTATCCTATGAAGACCCACCAACTGCCAAGGCTGCTGT
GGAGTGGTTTGATGGGAAAGATTTTCAAGGAAGCAAACTTAAGGTTTCTCTCGCTCAGAAGAAACCTCCAATGAACAGCA
TGCGGGGTGGTATGCCTCCCCGTGAGAGCAGAGGGATGCCACCGCCACTCCGTGGAGGTCCTGGGGCCCCATGGGTCGCA
TGGAAGGCCGTTGGAGGAGACAGAGGTGGCTTTCCCCCAAGAGGACCCCGGGGCTCCCGAGGGAACCCATCTGGAGGAGG
AAATGTCCAGCACCGAGCTGGGGACTGGCAGTGCCCCAATCCGGGGTGTGGAAACCAGAACTTCGCCTGGAGAACAGAAT
GCAACCAGTGTAAGGCCCCGAAGCCTGAAGGCTTCCTTCCACCACCCTTCCTGCCCCCGGGCGGTGACCGTGGCAGAGGC
GGCCCTGGTGGCATGCAGGGAGGAAGAGGTGGCCTCATGGACTGCAGTGGTCCAGGTGGGATGTTCAGAGGTGGCCGCAG
TGGAGACAGAGGGGGCTTCCGTGCTGGCCGGGGCATGGACCGAGGTGGCTTTGGTGGAGGAAGACGAGGCGGTCCTGGTG
GGCCCCCTGGACCTTTGATGGAACAGATGGGAGGAAGAAGAGGTGGGCGTGGAGGACATGGAAAAATGGATAAAGGCGAG
CACCGTCAGGAGTGCAGAGACCGGCCCTACTAG

Alignment

ORF - retro_cfam_133 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.74 %
• Parental protein coverage: 69. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SYSSTQPTSYDQSSYSQQNTYGQPSSYGQQSSYGQQSSYGQQPPTSYPPQTGSYSQAPSQYSQQSSSYGQ
          SY..T...S....SY.Q...Y.Q...YGQ.SSYGQQSSYGQQ......P.T.SY......YSQ..S.Y.Q
Retrocopy SYPPTSYSSTQPTSYDQ-SSYSQQNTYGQPSSYGQQSSYGQQSSYGQQPPT-SYPPQTGYYSQAPSQYSQ

Parental  QSSFRQDHPSSMGVYGQESGGFSGPGENRSMSGPDNRGRGRGGFDRG--GMSRGG--RGG---GRGGMGS
          QSS......S.........G.........S..G......G.....RG..G....G..RGG...GRGGMGS
Retrocopy QSSSYGQQSSFQQDHPSKMGVYGQESGGFSGPGENQSMSGTDNRGRGRGGFDHAGMSRGGRGGGRGGMGS

Parental  AGERGGFNKPGGPMDEGPDLDKGPPVDPDEDSDNSAIYVQGLNDNVTLDDLADFFKQCGVVKMNKRTGQP
          AGERGGFNKPGGPMDEGPDLD.GPPVDPDEDSDN.AIYVQGLNDNVTLDD.AD.FKQCG.VKMNKRTGQP
Retrocopy AGERGGFNKPGGPMDEGPDLDLGPPVDPDEDSDNNAIYVQGLNDNVTLDDVADLFKQCGIVKMNKRTGQP

Parental  MIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSMRGGMPPREGRGM
          MIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA.KKPPMNSMRGGMPPRE.RGM
Retrocopy MIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAQKKPPMNSMRGGMPPRESRGM

Parental  PPPLRGGPGGPGGPGGPMGRMGGRGGDRGGFPPRGPRGSRGNPSGGGNVQHRAGDWQCPNPGCGNQNFAW
          PPPLRGGPG.P.......G..G.RGG....FPPRGPRGSRGNPSGGGNVQHRAGDWQCPNPGCGNQNFAW
Retrocopy PPPLRGGPGAPWVAWKAVG--GDRGG----FPPRGPRGSRGNPSGGGNVQHRAGDWQCPNPGCGNQNFAW

Parental  RTECNQCKAPKPEGFLPPPFPPPGGDRGRGGPGGMRGGRGGLMDRGGPGGMFRGGRGGDRGGFRGGRGMD
          RTECNQCKAPKPEGFLPPPF.PPGGDRGRGGPGGM.GGRGGLMD..GPGGMFRGGR.GDRGGFR.GRGMD
Retrocopy RTECNQCKAPKPEGFLPPPFLPPGGDRGRGGPGGMQGGRGGLMDCSGPGGMFRGGRSGDRGGFRAGRGMD

Parental  RGGFGGGRRGGPGGPPGPLMEQMGGRRGGRGGPGKMDKGEHRQERRDRPY
          RGGFGGGRRGGPGGPPGPLMEQMGGRRGGRGG.GKMDKGEHRQE.RDRPY
Retrocopy RGGFGGGRRGGPGGPPGPLMEQMGGRRGGRGGHGKMDKGEHRQECRDRPY

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	0.84 RPM	77.74 RPM
SRP017611_brain	0.16 RPM	36.04 RPM
SRP017611_kidney	0.40 RPM	45.24 RPM
SRP017611_liver	0.07 RPM	33.94 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_133 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_133 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_133 has 0 orthologous retrocopies within eutheria group .

---

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,