RetrogeneDB ID: retro_cfam_1498

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:16281854..16282674(-)
• Located in intron of: ENSCAFG00000024991

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000031486
• Aliases: None
• Description: None

Sequence

>retro_cfam_1498
CGCGTGGCGCTGCTGCCCAGAGCCAACAAGGGCGTGGGTTCGCCACGGCGCAGCCGGTGCCGGCAGTTCTTGGGGTCTGG
GTGCTGGTGGCGCGGGACGGGGCACGGGGCCGGGCGGCCGTGCAGCAGCTCCAGGCCGAGGGCCGGAGCCCGCGCTCCCA
CCTGCTGGCATCGACCAGGAGCAGAGCATCCGCGCCCTGCGCGACCTGCTGCGCAAGGAGCACGCGGGCCTGGACCTGCT
GCTGCTCAACGACGCGGCCATCGCCTTCGAGACAATGATCCCACACCGTTTCGCGTGCAAGCAGAAGTGACCAGGAAAAC
AGACTTCTTTGGACCCTGAGGCGTGTGCACAGAACTGCTGCCTCTAACGAAAGCCCAAGGCAGAGTGGTGAACGTGTCTA
GCGGGGTGAGTGTCCGAGCCCTAGTTTAAAAGCTGCAGCCCAGAACGACAGCAGAAGTTTGGAAGTGAGGGCATCACAGA
GGGGGAGTTGGAGGGGCTCCTGAGCAGGTTCACGGAAGACACAAAGAAAGGCGTGCACAGGCATGAGGGCTGGCTTGATA
CCGCCTATGGAGTGACAAAAATCGGTGTCACTGTCCTGTCCAGAATCCATGCCAGGAAGCTGAGTGAGCAGAGGAGAGGT
GACAAGATCCTCCTGAATGCCTGCTGCCCTGGGTGGGTGAGAACAGACACGGCAGGACCTAATGCCCCTAAGAGCCCCGA
AGTAGGAGCAGAGACCCCTGTCTACTTGGCCCTTTTGCCCTCAGATTCTGAGGGGCCTCATGGAGAGTTTCTTACGGAGA
AAAAAAACGTTGAACAATGG

Alignment

ORF - retro_cfam_1498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.27 %
• Parental protein coverage: 98.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RVALVTGANKGIGFAIARELCRQFSGDV-VLTARDEARGRAAVQQLQAEGLSPRFHLL-DIDDLQSIRAL
          RVAL...ANKG.G....R..CRQF.G...VL.ARD.ARGRAAVQQLQAEG.SPR.HLL..ID..QSIRAL
Retrocopy RVALLPRANKGVG-SPRRSRCRQFLGSG<VLVARDGARGRAAVQQLQAEGRSPRSHLL<GIDQEQSIRAL

Parental  RDFLRKEYGGLDVLV-NNAGIAFKT-NDPTPFHIQAEVTMKTNFFGTRDVCTELLPLMKPQGRVVNV-SS
          RD.LRKE..GLD.L..N.A.IAF.T.NDPTPF..QAEVT.KT.FFG...VCTELLPL.K.QGRVVNV.S.
Retrocopy RDLLRKEHAGLDLLLLNDAAIAFET<NDPTPFRVQAEVTRKTDFFGP*GVCTELLPLTKAQGRVVNVSSG

Parental  V-VSVRALKSCSPELQQKFRSEAITEEELVGLMNKFVEDTKKGVHRNEGWPDNAYGVTKIGVTVLSRIHA
          V.VS....KSCSPE.QQKF.SE.ITE.EL.GL...F.EDTKKGVHR.EGW.D.AYGVTKIGVTVLSRIHA
Retrocopy V>VSEP*FKSCSPERQQKFGSEGITEGELEGLLSRFTEDTKKGVHRHEGWLDTAYGVTKIGVTVLSRIHA

Parental  RKLSEQRRDDKILLNACCPGWVRTDMAGPRAPKSPEEGAETPVYLALLPSDAEGPHGEFLME-KKVEQW
          RKLSEQRR.DKILLNACCPGWVRTD.AGP.APKSPE.GAETPVYLALLPSD.EGPHGEFL.E...VEQW
Retrocopy RKLSEQRRGDKILLNACCPGWVRTDTAGPNAPKSPEVGAETPVYLALLPSDSEGPHGEFLTEXXXVEQW

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	42.59 RPM
SRP017611_brain	0.00 RPM	25.09 RPM
SRP017611_kidney	0.00 RPM	85.65 RPM
SRP017611_liver	0.00 RPM	518.54 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1498 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1498 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1498 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	ENSCAFG00000031486	1 retrocopy	retro_cfam_1498 ,
Felis catus	ENSFCAG00000025135	1 retrocopy	retro_fcat_118,
Monodelphis domestica	ENSMODG00000021047	1 retrocopy	retro_mdom_278,