RetrogeneDB ID: retro_cfam_2091

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:62988092..62988938(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPSNAP1
• Ensembl ID: ENSCAFG00000012291
• Aliases: None
• Description: nipsnap homolog 1 (C. elegans) [Source:HGNC Symbol;Acc:7827]

Sequence

>retro_cfam_2091
ATGGCTCTGTGGCTGTGCAGCATCTCTGCAGCCGCGCAGCGGCTGCTGGGGAGCCCGAAGCCCCGTGCCAGGGATGTCGC
GGCTGCTGCATGCTTCTATTCCAAGGACAATGAAGGTAGCTGGTTCCGCTCCCTCTCTGTGCACAAGGTGGATCCCTGGA
AGGATGCCCACTCCACCCTGCTGTCCAAGACGGAAACCAGCAACCTCTACAAGATCCAGTTTCACAATGTGAAGCCTGAA
TGTCTGGATGCCTACAACAGCCTGACAGAGGCTGTGCTGCCCAAGCTGCACCTGGATGAGGACTACCCCTGCTCGTTCGT
GGGCAACTGGAACACATGGTACGGGGAGCAGGACCAGGCAGTACACCTGTGGCGATTCTCAGGCTGCTATCCAGTCCTCA
TGGACTGCATGAACAAGCTCAAAAGCAACAAGGAGTACCTGGAGTTCCAAAAAGAGCGGAGCCAGATGCTACTGTCGAGG
AGAAACCAGATGCTCCTTGAGTTCAGCTTCTGGAATGAGCCACAGCCCAGAGCAGGCCCCAACATCTATGAGCTGAGGAC
ATACAAGCTCAAGCCAGGAACCATGATTTAGTGGGGAAACAACTGGGCTCGGGCAATCAAGTACCGGCAAGAGAACCAGG
AGGCAGTAGGCGACTTCTTCTTGCAGATAGGAGAGCTCTACGTTGTACACCATCTCTGGGCCTATAAAGACCTGCAATCT
CGGGAAGAGACTCGAAATGCTGCCTGGAGAAAGAGGGGCTGGGACGAAAATATCTACTACACAGTCCCATTGGTGCGACA
CATGGAGTCTCGGATCATGATCCCTTCGAAGATCTGGCCTCTCCAG

Alignment

ORF - retro_cfam_2091 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.63 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPRLCSISAAARRLLGSPKPRAGDVAAAARLRIFYSKDNEGSWFRSLFVHKVDPRKDAHSTLLSKKETS
          MA..LCSISAAA.RLLGSPKPRA.DVAAAA....FYSKDNEGSWFRSL.VHKVDP.KDAHSTLLSK.ETS
Retrocopy MALWLCSISAAAQRLLGSPKPRARDVAAAA---CFYSKDNEGSWFRSLSVHKVDPWKDAHSTLLSKTETS

Parental  NLYKIQFHNVKPECLDAYNSLTEAVLPKLHLDEDYPCSLVGNWNTWYGEQDQAVHLWRFSGGYPALMDCM
          NLYKIQFHNVKPECLDAYNSLTEAVLPKLHLDEDYPCS.VGNWNTWYGEQDQAVHLWRFSG.YP.LMDCM
Retrocopy NLYKIQFHNVKPECLDAYNSLTEAVLPKLHLDEDYPCSFVGNWNTWYGEQDQAVHLWRFSGCYPVLMDCM

Parental  NKLKSNKEYLEFRKERSQMLLSRRNQMLLEFSFWNEPQPRAGPNIYELRTYKLKPGTMIEWGNNWARAIK
          NKLKSNKEYLEF.KERSQMLLSRRNQMLLEFSFWNEPQPRAGPNIYELRTYKLKPGTMI.WGNNWARAIK
Retrocopy NKLKSNKEYLEFQKERSQMLLSRRNQMLLEFSFWNEPQPRAGPNIYELRTYKLKPGTMI*WGNNWARAIK

Parental  YRQENQEAVGGFFSQIGELYVVHHLWAYKDLQSREETRNAAWRKRGWDENVYYTVPLVRHMESRIMIPLK
          YRQENQEAVG.FF.QIGELYVVHHLWAYKDLQSREETRNAAWRKRGWDEN.YYTVPLVRHMESRIMIP.K
Retrocopy YRQENQEAVGDFFLQIGELYVVHHLWAYKDLQSREETRNAAWRKRGWDENIYYTVPLVRHMESRIMIPSK

Parental  ISPLQ
          I.PLQ
Retrocopy IWPLQ

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	0.17 RPM	35.11 RPM
SRP017611_brain	0.08 RPM	36.20 RPM
SRP017611_kidney	0.40 RPM	91.73 RPM
SRP017611_liver	0.73 RPM	81.21 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2091 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2091 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2091 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012291	1 retrocopy	retro_cfam_2091 ,
Otolemur garnettii	ENSOGAG00000012167	1 retrocopy	retro_ogar_2741,
Pteropus vampyrus	ENSPVAG00000017876	1 retrocopy	retro_pvam_675,
Sus scrofa	ENSSSCG00000009988	1 retrocopy	retro_sscr_615,
Tupaia belangeri	ENSTBEG00000004614	3 retrocopies	retro_tbel_247, retro_tbel_4673, retro_tbel_968,