RetrogeneDB ID: retro_rnor_632

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:219421939..219422555(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nt5c3
• Ensembl ID: ENSRNOG00000005981
• Aliases: Nt5c3a, Nt5c3
• Description: 5'-nucleotidase, cytosolic III [Source:RefSeq peptide;Acc:NP_001101332]

Sequence

>retro_rnor_632
TACACTAGTGAAGCGGATCCTGTTCTCACTGTGGAAGAGAAGGTCCCTTACATGGTAAAGTGGTCTACTCAACCTCATGG
TTTGCCTGTTGACACAGACATACTAAAAGTCAAACTTAAAGATACTGTGGCACACTCTGATCTTATACTCAGAGAAGGAT
ATGAGAATCTCTTCAGTAAACTTCAACAGCACAGTACCCCCATGTTCGTATCTCTGGCTGGTATCAGTGCTATGCTTGAG
GAAGGTGTCTGTCAGGATGGAGTTTATCACTAAGGTGTCAAAGTAGCATCCAACTTCATACAAGTTGACGAAAATGGAGT
GCTGAAAGGATTCAAAGGAGAACTAAGTCGTGCATTCAAGAAACATAACGGTACCTTTAGGAGTATAGATTATTTCAGCC
CAATGGAAAGGAACAGCAACACCATTGTGCCTGGAGACCCCCAAGGGGACTTAAAGATGGTAGGTGGCATAGACAAATGT
TGAACACGTTCTGAAAATTAGGTATCTGAATGACAGCGTAGACGAGCTTTAAGAAAAACACGTGGGCTCGTATGATATTG
TTTTAGTAAAAGAACAGTCACCAGAGGTCGTCAACTCTATTTTACAGAAGACATTA

Alignment

ORF - retro_rnor_632 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.59 %
• Parental protein coverage: 69.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YAIEVDPVLTVEEKFPYMVEWYTKSHGLLIEQGIPKAKLKEIVADSDVMLKEGYENFFGKLQQHGIPVFI
          Y..E.DPVLTVEEK.PYMV.W.T..HGL.....I.K.KLK..VA.SD..L.EGYEN.F.KLQQH..P.F.
Retrocopy YTSEADPVLTVEEKVPYMVKWSTQPHGLPVDTDILKVKLKDTVAHSDLILREGYENLFSKLQQHSTPMFV

Parental  FSAGIGDVLEEVIRQAGVYHSNVKVVSNFMDFDENGVLKGFKGELIHVFNKHDGALKNTDYFSQLKDNSN
          ..AGI...LEE...Q.GVYH..VKV.SNF...DENGVLKGFKGEL...F.KH.G.....DYFS....NSN
Retrocopy SLAGISAMLEEGVCQDGVYH*GVKVASNFIQVDENGVLKGFKGELSRAFKKHNGTFRSIDYFSPMERNSN

Parental  IILLGDSQGDLRMADGV-ANVEHILKIGYLNDRVDELLEKYMDSYDIVLVKEESLEVVNSILQKTL
          .I..GD.QGDL.M..G...NVEH.LKI.YLND.VDEL.EK...SYDIVLVKE.S.EVVNSILQKTL
Retrocopy TIVPGDPQGDLKMVGGI>TNVEHVLKIRYLNDSVDEL*EKHVGSYDIVLVKEQSPEVVNSILQKTL

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
SRP017611_brain	0.00 RPM	24.88 RPM
SRP017611_kidney	0.00 RPM	20.52 RPM
SRP017611_liver	0.00 RPM	8.88 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_632 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_632 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_632 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,