RetrogeneDB ID: retro_rnor_1023

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:89298168..89299521(+)
• Located in intron of: ENSRNOG00000025645

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tmem161b
• Ensembl ID: ENSRNOG00000032414
• Aliases: Tmem161b, RGD1309660
• Description: None

Sequence

>retro_rnor_1023
TTGAGATGGTATCAACACCCTTCCGAAGAAGAATTAAGAATCCTTGCAGGGAAGCAGCAGAAAGGAAAAAGTAAAAAAGA
CAGAAAATACAATGGCCATATTGAAAATAAGCCACTGACCATTCCAAAAGACATTGACCTTCATCTAGAAACCAAGTCCA
TTACAGAAGTGGATACTTTAGCACTGCATTACTTTCCAGAATACCAGTGGCTGGTGGACTTCACGGTGGCTGCTACTGTT
GTGTATTTAGTAACTGAAGTCTATTACAGCTTTATGAAGCCCACACAGGAAATGAATATCAGCTTAGTCTGGTGCCTCCT
GGTTTTGTCTTTTGCAATCAAAGTTCTATTTTCATTAACTACACACTATTTTAAAGTAGAAGATGGAGGTGAGAGGTCAG
TTTGTGTCACCTTTGGATTTTTTTTCTTCGTTAAAGCAATGGCAGTTTTGATCGTAACAGAGAACTACCTGGAGTTTGGA
CTTGAAACAGGGTTTACAAATTTTTCAGACACTGCGATGCAGTTTCTTGAAAAGCAAGGTTTAGAATCTCAGGGTCCTGT
TTCAAAACTTACTTTCAAATTTTTCCTGGCTGTTTTCTGTTCACTCATTGGGGCTTTTTTGACATTTCCTGGATTACGGC
TGGCTCAAATGCATCTGGATGCCCTGAATTTGGCAACAGAAAAAATTACACAAACATTACTTCATATCAACTTCTTGGCA
CCTTTATTTATGGTTCTGCTCTGGGTGAAACCAATCACCAAAGACTACATCATGAACCCACCATTGGGTAAAGAGAGTGT
CCCTTTAATGACAGAAGCCACATTCGATACTCTTCGACTCTGGTTAATAGTTCTGCTATGTGTTTTGCGGTTGGCCATGT
TGCGAAGTCACTTGCAAGCGTATTTAAACTTGGCCCAGAAATGTGTGGATCAAATGAAGAAAGAAGCAGGCCGAATAAGT
ACAGTGGAGCTACAGAAAATGGTAGCATGAGTCTTTTATTACCTGTGTGTCATTGCCCTGCAATATGTGGCACCTCTGGT
GATGCTGCTTCACATGACTCTGCTTCTGAAAACACTAGGTAATCATTCCTGGGGGATTTATCCAGAAGCTGTCTCTCCCT
TGCCAGTGGATAATAATCTCCCATCCAACTTGGTTTACCCTGAACTACCATCACCTGATGGGAAGATGAAGGTAACTGTT
ACGCAAATCACAGTGGCGTTGAGCAGCTTAAAAAACATCTTCACGCCTCTCCTTTTTCGAGGACTTCTGTCATTTTTGAC
ATGGTGGATTGCTGCTTGCCTCTTTTCTACAAGCCTTTTTGGGCTTTTCTATCATCAGTATCTGACAGTGGCA

Alignment

ORF - retro_rnor_1023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.45 %
• Parental protein coverage: 97.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRWYQHPSEEELRILAGKQQKGKSKKDRKYNGHIENKPLTIPKDIDLHLETKSVTEVDTLALHYFPEYQW
          LRWYQHPSEEELRILAGKQQKGKSKKDRKYNGHIENKPLTIPKDIDLHLETKS.TEVDTLALHYFPEYQW
Retrocopy LRWYQHPSEEELRILAGKQQKGKSKKDRKYNGHIENKPLTIPKDIDLHLETKSITEVDTLALHYFPEYQW

Parental  LVDFTVAATVVYLVTEVYYSFMKPTQEMNISLVWCLLVLSFAIKVLFSLTTHYFKVEDGGERSVCVTFGF
          LVDFTVAATVVYLVTEVYYSFMKPTQEMNISLVWCLLVLSFAIKVLFSLTTHYFKVEDGGERSVCVTFG.
Retrocopy LVDFTVAATVVYLVTEVYYSFMKPTQEMNISLVWCLLVLSFAIKVLFSLTTHYFKVEDGGERSVCVTFGX

Parental  FFFVKAMAVLIVTENYLEFGLETGFTNFSDTAMQFLEKQGLESQGPVSKLTFKFFLAVFCSLIGAFLTFP
          ..FVKAMAVLIVTENYLEFGLETGFTNFSDTAMQFLEKQGLESQGPVSKLTFKFFLAVFCSLIGAFLTFP
Retrocopy XXFVKAMAVLIVTENYLEFGLETGFTNFSDTAMQFLEKQGLESQGPVSKLTFKFFLAVFCSLIGAFLTFP

Parental  GLRLAQMHLDALNLATEKITQTLLHINFLAPLFMVLLWVKPITKDYIMNPPLGKESVPLMTEATFDTLRL
          GLRLAQMHLDALNLATEKITQTLLHINFLAPLFMVLLWVKPITKDYIMNPPLGKESVPLMTEATFDTLRL
Retrocopy GLRLAQMHLDALNLATEKITQTLLHINFLAPLFMVLLWVKPITKDYIMNPPLGKESVPLMTEATFDTLRL

Parental  WLIVLLCVLRLAMMRSHLQAYLNLAQKCVDQMKKEAGRISTVELQKMVARVFYYLCVIALQYVAPLVMLL
          WLIVLLCVLRLAM.RSHLQAYLNLAQKCVDQMKKEAGRISTVELQKMVA.VFYYLCVIALQYVAPLVMLL
Retrocopy WLIVLLCVLRLAMLRSHLQAYLNLAQKCVDQMKKEAGRISTVELQKMVA*VFYYLCVIALQYVAPLVMLL

Parental  HMTLLLKTLGNHSWGIYPEAVSPLPVDNNLPSNLVYPELPSPDGKMKVTVMQITVALSSLKNIFTPLLFR
          HMTLLLKTLGNHSWGIYPEAVSPLPVDNNLPSNLVYPELPSPDGKMKVTV.QITVALSSLKNIFTPLLFR
Retrocopy HMTLLLKTLGNHSWGIYPEAVSPLPVDNNLPSNLVYPELPSPDGKMKVTVTQITVALSSLKNIFTPLLFR

Parental  GLLSFLTWWIAACLFSTSLFGLFYHQYLTVA
          GLLSFLTWWIAACLFSTSLFGLFYHQYLTVA
Retrocopy GLLSFLTWWIAACLFSTSLFGLFYHQYLTVA

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	0.79 RPM	9.92 RPM
SRP017611_kidney	0.84 RPM	7.68 RPM
SRP017611_liver	0.94 RPM	5.45 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_rnor_1023 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CB789067	89298563	89298983	100	419	0	418

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1023 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1023 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010857	1 retrocopy	retro_cjac_2671,
Homo sapiens	ENSG00000164180	1 retrocopy	retro_hsap_560,
Gorilla gorilla	ENSGGOG00000005684	1 retrocopy	retro_ggor_506,
Macaca mulatta	ENSMMUG00000009319	1 retrocopy	retro_mmul_719,
Nomascus leucogenys	ENSNLEG00000013645	1 retrocopy	retro_nleu_2224,
Pan troglodytes	ENSPTRG00000017064	1 retrocopy	retro_ptro_419,
Rattus norvegicus	ENSRNOG00000032414	1 retrocopy	retro_rnor_1023 ,
Ictidomys tridecemlineatus	ENSSTOG00000027831	2 retrocopies	retro_itri_1419, retro_itri_1787,