RetrogeneDB ID: retro_cfam_975

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:4194574..4195834(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM114A2
• Ensembl ID: ENSCAFG00000017653
• Aliases: None
• Description: family with sequence similarity 114, member A2 [Source:HGNC Symbol;Acc:1333]

Sequence

>retro_cfam_975
CAGGAGACTGTTTCCAAAGATGTACCTCAGACTGGATGGGGATATTGGGGCAGCTGGGGCAAGTGCTTGCTCTCTTCAGC
CTCAGCTACAGTAGCTACAGTAAGACAAGGTATTTCAAATGTCATTGAGAAGGCAGAGACTTCTCTTGGAATTCCTAGTC
CCAGTGAAATTTCAACTGAAGTCCAGTATGCAGCAGGAGAGACAAATGCCAATGAGAATGCAAACTCCTCCTCATTGATT
GAGCCATTTGGTGTATTTTCAACCATCTCTACTGCTGTTCAAACCACAGGAAAGAGCGTGATCATTGGGGGTTTGGATGC
CTTAGAATTCATTGGGAAAAAGACAATGGATGTAATAGCAGAAGGGGATCCTGGATTTAAAAGAACCAAGGGTCTGATGA
ACCGGAATTCTACATTGTCTCAGGTTTTACGAAAGGCAAAGGAGAAAGAAGAGCTACGGACCTCCAATGAGGTTACCTTG
GAAACGGACAAGAAAACTCATTATGGGCTCCTTTTTGATGAATTTCAAGGCCTTTCGCATCTGGAAGCTCTGGAGATGCT
TTCACGAGAAAGTGAAATAAAGGTGAAATCTATTCTTAATTCTTTAAGTGGAGAAGAACTACAGACTCTAAAACTTGAAT
TGGAGCAACTCAAGGAAGCATTTTCTCTAGCAGAGTTCTGTGAGGAAGAGGAAGAATAGAAAAAAGATGACGAAGACTTT
ACCAAAGAAATAACAGAGCTATTTTCCCAGCTGCATGTCTCCTCCAAACCTGAGAAACTTACCAAGGCAAGGAATACTGC
CTACGAATGGATCAGTACATCTCTGGCCAAGCCATCAGAAGAGAAGGAAGATGGAGAGAAACAGTTGGAAACAGAAAAAA
TTGAGCAAATCAGTAAAAATTCAATAGAGGATATCCATGCATTTGCAATCCGGAGCCTAGCAGAGCTGACGCTGTTTCAC
AAAACAGCGGCTCTGGTTCTGCATGGCCAGAAGCAGGAAGTGACAGCCATAGAAAGAAGCAGAACTTTTTCCCAGATGAC
AATTGTGTTGTGTAAAGAGTTGTCTTCTCTGTCTAAAGAGTTCACCACTTGCCTAACAACTGCTGGGGTCAAAGAAAAGG
CAGACATCCTTAATCCCCTAGTCACTGCAGTATTTCTGGAGGCATCAAACAGTGCTTCCTATATGCAGGATGCCTTTCAG
CTGCTCTTACCTGTGCTAGAGATCTCTCTCATTGAGAACAAAACTGAATTACCAGAGGCA

Alignment

ORF - retro_cfam_975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.18 %
• Parental protein coverage: 84.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KETVSKDVPQTGWGYWGSWGKSLLSSASATVATVGQGISNVIEKAETSLGIPSPSEISTEVQYAAGETNA
          .ETVSKDVPQTGWGYWGSWGK.LLSSASATVATV.QGISNVIEKAETSLGIPSPSEISTEVQYAAGETNA
Retrocopy QETVSKDVPQTGWGYWGSWGKCLLSSASATVATVRQGISNVIEKAETSLGIPSPSEISTEVQYAAGETNA

Parental  NENANSSSLIGPFGVFSTISTAVQTTGKSVISGGLDALEFIGKKTMDVIAEGDPGFKRTKGLMNRNSTLS
          NENANSSSLI.PFGVFSTISTAVQTTGKSVI.GGLDALEFIGKKTMDVIAEGDPGFKRTKGLMNRNSTLS
Retrocopy NENANSSSLIEPFGVFSTISTAVQTTGKSVIIGGLDALEFIGKKTMDVIAEGDPGFKRTKGLMNRNSTLS

Parental  QVLREAKEKEELWTSNEVTLETDKKTHYGLLFDEFQGLSHLEALEMLSRESEIKVKSILNSLSGEELQTL
          QVLR.AKEKEEL.TSNEVTLETDKKTHYGLLFDEFQGLSHLEALEMLSRESEIKVKSILNSLSGEELQTL
Retrocopy QVLRKAKEKEELRTSNEVTLETDKKTHYGLLFDEFQGLSHLEALEMLSRESEIKVKSILNSLSGEELQTL

Parental  KLELEQLKEAFSLAEFCEEEEEEKKDDEDFTKEITELFSQLHVSSKPEKLTKARNTAYEWISTSLAKPSE
          KLELEQLKEAFSLAEFCEEEEE.KKDDEDFTKEITELFSQLHVSSKPEKLTKARNTAYEWISTSLAKPS.
Retrocopy KLELEQLKEAFSLAEFCEEEEE*KKDDEDFTKEITELFSQLHVSSKPEKLTKARNTAYEWISTSLAKPS-

Parental  EKEDGEKQLETEKIEQISKNSIEDIHAFAIRSLAELTACSIELFHKTAALVLHGQKQEVTAIERSRTLSQ
          ..E..E........E.I...S...I....I...A........LFHKTAALVLHGQKQEVTAIERSRT.SQ
Retrocopy --EEKEDGEKQLETEKIEQISKNSIED--IHAFAIRSLAELTLFHKTAALVLHGQKQEVTAIERSRTFSQ

Parental  MTIVLCKELSSLSKEFTTCLTTAGVKEKADILNPLITAVFLEASNSASYIQDAFQLLLPVLEISLIENKT
          MTIVLCKELSSLSKEFTTCLTTAGVKEKADILNPL.TAVFLEASNSASY.QDAFQLLLPVLEISLIENKT
Retrocopy MTIVLCKELSSLSKEFTTCLTTAGVKEKADILNPLVTAVFLEASNSASYMQDAFQLLLPVLEISLIENKT

Parental  ELPEA
          ELPEA
Retrocopy ELPEA

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	0.00 RPM	21.80 RPM
SRP017611_brain	0.16 RPM	22.07 RPM
SRP017611_kidney	0.00 RPM	35.73 RPM
SRP017611_liver	0.00 RPM	12.25 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_975 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_975 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_975 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017653	1 retrocopy	retro_cfam_975 ,
Gorilla gorilla	ENSGGOG00000007198	1 retrocopy	retro_ggor_889,
Tupaia belangeri	ENSTBEG00000004757	1 retrocopy	retro_tbel_3070,