RetrogeneDB ID: retro_cfam_482

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:25464189..25464738(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCAP31
• Ensembl ID: ENSCAFG00000019245
• Aliases: None
• Description: B-cell receptor-associated protein 31 [Source:HGNC Symbol;Acc:16695]

Sequence

>retro_cfam_482
CGTTGGCTGCGGGGAGCTCGGAAACAAGCTCGCATCCCACTGTTGGGAACCTTCTAGCAACAGCATGAGTCTGCAGTGGA
CTGCAGTCGCCACCTTCCTCTATGCAGAGGTCTCTGCTGTGCTGCTTCTCCGCATTCCCTTCATTTCTCCCAAAAGATGG
CAGAAGATTTTCAAGTCTGCCTGGTGGAGTTGGTAGTAACTTATGGCAACACCTTCTTTGTAGTCCTCATTGTCATCCTT
GTGCTGCTGGTCATTGATGCTGTACGTGAGATTCGGAAGTACGACGACGTGACAGAGAAGGTGAACCTGCAGAATAATCC
TGGGGCTGTGGAACACTTCCACATGAAGCTTTTCCGTGCCCAGAGGAATCTCTATGTTGCTGGCTTTTCCTTGCTGCTGT
CCTTCCTGCTTAGAGGCCTGGTGACTCTCATCTCACAGCAGGCCACGCTGCTGGTGGCCAATGAAGCCTTTAAAAAGCAG
GCAGAGAGTGCCAGTGAGGCGGCCAAGAAGTACATGGAAGAGAATGACCAGCTGAAGAAGGAAGCTGCT

Alignment

ORF - retro_cfam_482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.51 %
• Parental protein coverage: 68.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVLEGA-GNKLASHCWKPSSNSMSLQWTAVATFLYAEVFAVLLLCIPFISPKRWQKIFKSR-LVELVVTY
          R.L.GA.GNKLASHCW.PSSNSMSLQWTAVATFLYAEV.AVLLL.IPFISPKRWQKIFKS..LVELVVTY
Retrocopy RWLRGA>GNKLASHCWEPSSNSMSLQWTAVATFLYAEVSAVLLLRIPFISPKRWQKIFKSA<LVELVVTY

Parental  GNTFFVVLIVILVLLVIDAVREIRKYDDVTEKVNLQNNPGAVEHFHMKLFRAQRNLYIAGFSLLLSFLLR
          GNTFFVVLIVILVLLVIDAVREIRKYDDVTEKVNLQNNPGAVEHFHMKLFRAQRNLY.AGFSLLLSFLLR
Retrocopy GNTFFVVLIVILVLLVIDAVREIRKYDDVTEKVNLQNNPGAVEHFHMKLFRAQRNLYVAGFSLLLSFLLR

Parental  RLVTLISQQATLLASNEAFKKQAESASEAAKKYMEENDQLKKEAA
          .LVTLISQQATLL..NEAFKKQAESASEAAKKYMEENDQLKKEAA
Retrocopy GLVTLISQQATLLVANEAFKKQAESASEAAKKYMEENDQLKKEAA

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	63.96 RPM
SRP017611_brain	0.00 RPM	62.40 RPM
SRP017611_kidney	0.00 RPM	154.92 RPM
SRP017611_liver	0.00 RPM	39.52 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_482 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_482 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_482 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019245	1 retrocopy	retro_cfam_482 ,
Callithrix jacchus	ENSCJAG00000011348	1 retrocopy	retro_cjac_2552,
Echinops telfairi	ENSETEG00000008662	1 retrocopy	retro_etel_1522,
Macropus eugenii	ENSMEUG00000007345	3 retrocopies	retro_meug_1017, retro_meug_1867, retro_meug_208,
Monodelphis domestica	ENSMODG00000008300	2 retrocopies	retro_mdom_1110, retro_mdom_24,
Sarcophilus harrisii	ENSSHAG00000009111	1 retrocopy	retro_shar_31,