RetrogeneDB ID: retro_cfam_1295

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 29:40096893..40097433(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C3A
• Ensembl ID: ENSCAFG00000003154
• Aliases: NT5C3A, NT5C3
• Description: 5'-nucleotidase, cytosolic IIIA [Source:HGNC Symbol;Acc:17820]

Sequence

>retro_cfam_1295
ATGCCTCATCACGATTCTGCTGTACATGTGAAAATGATGCAAGAATTCCAGAGACGTTTGGTTCAGATGAAGACCACTGC
AGGAGTGGAAGAAATGACCCGTGGTTTCATTAAGGAAGGAGCTGCCAAGCTTCAGATAATAACGACAGACTTTGATATGT
TACCGAGTAGATTTTCCTATGAAGGGAAAAGATGCCCACCATGTTATTATGTCATTGACAACAGTAAACTGGTCACAAAT
GAATGTTGGGAAAAGTTGCTGCAACTAAAGGAAAAATACTAGGCTGTTGAAATCGATCCTCTTCTTGCCGTAGAAGAGAA
GTTCCCCTATATGTTAGGATGGTATATACTGAGTCACACGGTTTGCTTGTTGAGCAGGTGTTACCAAAAGCTAAATTTCA
AGAAATTGTGGTAGGATCTGATGTTATGCTCAAGGAAGGGTGTGAGAATTTCTTTGTTAAACTCCAACAATACGGTATCC
CCTGTGTTCATATTTTCAGCTGGTATTGGTCACATAGCAGAGGAGGTGATCTATCAAGCC

Alignment

ORF - retro_cfam_1295 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.33 %
• Parental protein coverage: 59.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPNQDSAVHVKMMPEFQRSSVRIKNPARVEEIICGLIKGGAAKLQIIT-DFDMTLSRFSYEGKRCPTCHY
          MP..DSAVHVKMM.EFQR..V..K..A.VEE...G.IK.GAAKLQIIT.DFDM..SRFSYEGKRCP.C.Y
Retrocopy MPHHDSAVHVKMMQEFQRRLVQMKTTAGVEEMTRGFIKEGAAKLQIITTDFDMLPSRFSYEGKRCPPCYY

Parental  VIDNSKLVTDECRKKLLQLKEKYYAIEIDPVLTMEEKYPYMVEWYTKSHGL-LVEQALPK-AKLKEIVAE
          VIDNSKLVT.EC..KLLQLKEKY.A.EIDP.L..EEK.PYM..WY..SH...L......K.AK..EIV..
Retrocopy VIDNSKLVTNECWEKLLQLKEKY*AVEIDPLLAVEEKFPYMLGWYILSHTVCLLSRCYQK<AKFQEIVVG

Parental  SDVMLKEGYENFFDKLQEYGI-PVFIFSAGIGDILEEVIHQA
          SDVMLKEG.ENFF.KLQ.YGI.PVFIFSAGIG.I.EEVI.QA
Retrocopy SDVMLKEGCENFFVKLQQYGI>PVFIFSAGIGHIAEEVIYQA

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	14.36 RPM
SRP017611_brain	0.00 RPM	20.40 RPM
SRP017611_kidney	0.00 RPM	29.65 RPM
SRP017611_liver	0.00 RPM	27.12 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1295 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1295 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1295 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006624	1 retrocopy	retro_amel_875,
Bos taurus	ENSBTAG00000016709	1 retrocopy	retro_btau_1465,
Canis familiaris	ENSCAFG00000003154	1 retrocopy	retro_cfam_1295 ,
Equus caballus	ENSECAG00000011777	1 retrocopy	retro_ecab_1118,
Homo sapiens	ENSG00000122643	1 retrocopy	retro_hsap_3084,
Gorilla gorilla	ENSGGOG00000028164	1 retrocopy	retro_ggor_2119,
Mustela putorius furo	ENSMPUG00000005546	2 retrocopies	retro_mputfur_1175, retro_mputfur_577,
Pteropus vampyrus	ENSPVAG00000013182	2 retrocopies	retro_pvam_148, retro_pvam_706,
Rattus norvegicus	ENSRNOG00000005981	1 retrocopy	retro_rnor_632,
Sus scrofa	ENSSSCG00000022912	1 retrocopy	retro_sscr_540,
Ictidomys tridecemlineatus	ENSSTOG00000026363	2 retrocopies	retro_itri_1325, retro_itri_682,