RetrogeneDB ID: retro_cfam_256

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:35357063..35358110(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMARCD2
• Ensembl ID: ENSCAFG00000012708
• Aliases: None
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 [Source:HGNC Symbol;Acc:11107]

Sequence

>retro_cfam_256
GCCATCAAAAAGCCTCTGACACAAAAACGGAAGCTGCGCATCTATACTTCCAATACGTTCAGTCCCAGCAAGGCAGAAGG
CGATACTGCGGGCACCGCGGGGCCCCCTGGGGGAACCCCTGCAGGGGACAAGGTGGCTTCCTGGGAACTCCGAGTGGAGG
GAAAACTGCTGGATGATCCTAGCAAACAGAAGAGGAAGTTTTCTTCATTCTTTAAGAGCCTCGTCATTGAGCTGGACAAA
GAGTTATACGGGCCTGACAACCACCTGGTAGAGTGGCACTGGATGCCCACCACCCAGGAGACTGATGGCCTCCAGGTCAA
ACGGCCTGGAGACCTCAACGTCAAGTGCACCCTCCTGCTCATGCTAGATCATCAGCCTCCCCAGTACAAGTTGGACCCCC
GACTGGCAAGGCTGCTGGGGGTGCACACACAGACAAGGGCGGCCATCATGCAGGCTCTTTGGCTTTATATCAAACACAAC
CAACTGCAGGACGGGCACGAGCACGAGTACATCAATTGCAACCGTTACTTCCGCCAGATCTTCAGTTGTGGCCGACTTCG
TTTCTCTGAGATTCCCATGAAGCTGGCTGGGTTGCTGCAGCATCCAGACCCCATTGTCATCAACCATGTCATTAGCGTAG
ACCCTAACAACCAGAAGAAGACAGCATGCTACGACATTGATGTGGAGGTAGATGACCCACTCAAGGCCCAGATGAGCAAT
TTTCTGGCCTCTACCACCAATCAGCAGGAGATTGCCTCCCTCGATGTCGAGATCCATGAGACCATTGAGTCCATCAACCA
GCTGAAGACCCAGAGGGATTTCATGCTCAGCTTTAGCACGGACCCTCAGGACTTCATCCAGGAATGGCTCTGTTCTCAGC
GCCGAGACCTCAAGATCATCACTGATGTGATTGGGAATCCTGGGGAGGAGAGACGAGCTGCTTTCTACCACCAGCCCTGG
GCCCAGGAAGCAGTGGGGAAGCACATCTTTGCCAAGGTGCAGCAGCGAAGGCAAGAACTGGAACAGGTGCTGGGAATCCG
CTTGACC

Alignment

ORF - retro_cfam_256 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.13 %
• Parental protein coverage: 65.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AIKKPLTQKRKLRIYISNTFSPSKAEGDNAGTAGPPGGTPAGDKVASWELRVEGKLLDDPSKQKRKFSSF
          AIKKPLTQKRKLRIY.SNTFSPSKAEGD.AGTAGPPGGTPAGDKVASWELRVEGKLLDDPSKQKRKFSSF
Retrocopy AIKKPLTQKRKLRIYTSNTFSPSKAEGDTAGTAGPPGGTPAGDKVASWELRVEGKLLDDPSKQKRKFSSF

Parental  FKSLVIELDKELYGPDNHLVEWHRMPTTQETDGFQVKRPGDLNVKCTLLLMLDHQPPQYKLDPRLARLLG
          FKSLVIELDKELYGPDNHLVEWH.MPTTQETDG.QVKRPGDLNVKCTLLLMLDHQPPQYKLDPRLARLLG
Retrocopy FKSLVIELDKELYGPDNHLVEWHWMPTTQETDGLQVKRPGDLNVKCTLLLMLDHQPPQYKLDPRLARLLG

Parental  VHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSEIPMKLAGLLQHPDPIVINHV
          VHTQTRAAIMQALWLYIKHNQLQDGHE.EYINCNRYFRQIFSCGRLRFSEIPMKLAGLLQHPDPIVINHV
Retrocopy VHTQTRAAIMQALWLYIKHNQLQDGHEHEYINCNRYFRQIFSCGRLRFSEIPMKLAGLLQHPDPIVINHV

Parental  ISVDPNDQKKTACYDIDVEVDDPLKAQMSNFLASTTNQQEIASLDVKIHETIESINQLKTQRDFMLSFST
          ISVDPN.QKKTACYDIDVEVDDPLKAQMSNFLASTTNQQEIASLDV.IHETIESINQLKTQRDFMLSFST
Retrocopy ISVDPNNQKKTACYDIDVEVDDPLKAQMSNFLASTTNQQEIASLDVEIHETIESINQLKTQRDFMLSFST

Parental  DPQDFIQEWLRSQRRDLKIITDVIGNPEEERRAAFYHQPWAQEAVGRHIFAKVQQRRQELEQVLGIRLT
          DPQDFIQEWL.SQRRDLKIITDVIGNP.EERRAAFYHQPWAQEAVG.HIFAKVQQRRQELEQVLGIRLT
Retrocopy DPQDFIQEWLCSQRRDLKIITDVIGNPGEERRAAFYHQPWAQEAVGKHIFAKVQQRRQELEQVLGIRLT

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	36.20 RPM
SRP017611_brain	0.00 RPM	10.48 RPM
SRP017611_kidney	0.00 RPM	33.94 RPM
SRP017611_liver	0.22 RPM	60.04 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_256 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_256 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_256 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012708	1 retrocopy	retro_cfam_256 ,
Callithrix jacchus	ENSCJAG00000019528	1 retrocopy	retro_cjac_2323,
Mustela putorius furo	ENSMPUG00000014835	1 retrocopy	retro_mputfur_89,
Sarcophilus harrisii	ENSSHAG00000013118	1 retrocopy	retro_shar_464,
Tursiops truncatus	ENSTTRG00000006988	1 retrocopy	retro_ttru_1394,