RetrogeneDB ID: retro_cfam_1542

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 34:5611957..5612416(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAP29
• Ensembl ID: ENSCAFG00000015201
• Aliases: None
• Description: synaptosomal-associated protein, 29kDa [Source:HGNC Symbol;Acc:11133]

Sequence

>retro_cfam_1542
ACGCGCGCGGACAGGCGGCCACGTGGGCAGGAGCTGATGCGCGTGGCCCAGGCCAGGGCCGCCGGCACCGAGGGTCCCTG
CCCCTCCTGTGCGAGTCCGGCGAGGTCGGCGTCGCGTCTGCAGAGGAGCTCGTCCGCCCTCGGGGGTCTTAGAACGCCGG
GGAAGATGCGGGACAAGGTGGATCAAGATTCGGAGACCGGCCAGAAGCACGTTAACAGCCTAAGAGCATGTTGGGGGGGT
TCGTCGATTACTTCGAGTCCAAACCAGCAGAGACGCCCCCCGAACAGAAAGGCACCCTTGCCCCCCAGCCTAACAGCGGA
TTGAAAGGAGCGTAAGTACCAGTAAAGCACAGGAGGCGCCATCCAGGGCAGCCACCCAAACCTCGGGAAGCCGAAGGGCT
CAGGCTCTTTCCCTGGAGGCGAGCACCGAGGCTTGCCCGAGGAACCCCCACCTTCGAGC

Alignment

ORF - retro_cfam_1542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.73 %
• Parental protein coverage: 60.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  TPADRQQYLRQEVMRVAQATAASTER-SLSLMYESEKVGVASSEELVRQRG-VLERTE-KMVDKMDQDLK
          T.ADR.....QE.MRVAQA.AA.TE..SL.L..ES..VGVAS.EELVR.RG.VLER...KM.DK.DQD..
Retrocopy TRADRRPR-GQELMRVAQARAAGTEG<SLPLLCESGEVGVASAEELVRPRG<VLERRG<KMRDKVDQDSE

Parental  TSQKHINSI-KSMFGGFVNYFKSKPTETPPEQNGTLAPQANS-RLKEAISTSKAQEA-QYQASHPNLRKL
          T.QKH.NS..KSM.GGFV.YF.SKP.ETPPEQ.GTLAPQ.NS.R.....STSKAQEA...Q.SHPNL.K.
Retrocopy TGQKHVNSL<KSMLGGFVDYFESKPAETPPEQKGTLAPQPNS<RIERSVSTSKAQEA<AIQGSHPNLGKP

Parental  NDSDSFPGGTGSAASTEAYPKN
          ..S.SFPGG.......E..P..
Retrocopy KGSGSFPGGEHRGLPEEPPPSS

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	82.23 RPM
SRP017611_brain	0.00 RPM	44.14 RPM
SRP017611_kidney	0.00 RPM	57.19 RPM
SRP017611_liver	0.00 RPM	37.49 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1542 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1542 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1542 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015201	1 retrocopy	retro_cfam_1542 ,
Cavia porcellus	ENSCPOG00000003137	1 retrocopy	retro_cpor_1442,
Dasypus novemcinctus	ENSDNOG00000005913	4 retrocopies	retro_dnov_1401, retro_dnov_1855, retro_dnov_2001, retro_dnov_2364,
Nomascus leucogenys	ENSNLEG00000000108	1 retrocopy	retro_nleu_2645,
Otolemur garnettii	ENSOGAG00000013003	1 retrocopy	retro_ogar_3493,