RetrogeneDB ID: retro_rnor_1500

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:74561982..74563195(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Etv5
• Ensembl ID: ENSRNOG00000001785
• Aliases: None
• Description: ETS translocation variant 5 [Source:RefSeq peptide;Acc:NP_001100552]

Sequence

>retro_rnor_1500
ACCAAGATCAAACCCGAGCTGCACAGCCCTCCTCTGAGTTGTCCTCCTGTAGCCATGAGCAGGCTCTTGGTGCTAAGTAT
GGGGAAAAGTGCCTCTACAACTATTGTGCCTATGACAGGAAGCCTCCCTTTGGGTTCAAGCCATTAACCCCACCCGCCAC
TCCTTTACCACCCACCCATTAGAATTCCCTATTTCCCCCACTTAAGGCAACTCTGCCCACCTCAGCTCTTGCCCCTGGAG
CCTGTTCAGTTCAAGGGGTGGGTCCTGTCCCAGCCCTCACTCCCTTCCAGAACCTGGATCACAGCAGCATACATTTGCGG
TCCCCCGGTCACCATATCAACCCTGCAAATGCCAAAGATGATGCCCGAAAGCCAGTATCCATCAGAACAGAGATTTCAGC
GACAGCTGTCTGAGCCCTGCCGCCCCTTCCCTCCTCAGTCAGGAGTTCCTGGAGATACTCACCCCAGCTACCAAAGGCAG
ATGTTAGAGCTCGTTGTCCCCGCAGCTTTGCCACCCCTTCAGGGATTCAAGCAGGAATACCACAATCCACACTATGAACA
TGGGATCCCTGGAATGCCTGGTCCCCCAGCACATGGGTTCCAGTCACCCTTGGGAATCAAGCAGTAGCCCCGAGATTACT
GTGCTGACTCAGAAGTGCTAACTGCCAGTCACCCTATATGAGAGGCAGGTATTTTTCCAGCAACCATGAAGGATTCACAT
ATGAAAAGGACCCCAGGCTATACTATACTTTGATGATACTTGCGTGATGCCGGAAAGACTGGAAGGCAAAGTCAAGAAGG
AGCCCACCATGTATCAAGAGGGGCCCCCTTACCAGAGGCAAGGCTCTCTGCAGCTGTGGCAGTTTCTCGCCACCCTTCTG
GATGACCCAGCCAATGCCCACTTCATCGCCTGGACTGGACAAGACGTGGAGTTTAAGCTTACAGAACCGGAAGAGGTTGC
TGGTCGTTGGGGTATTCAGAAGAACCAGCCAGCCATGAACTATGACAAGCTGAGCCGTTCCCTGCGCTATTACTATGAAA
AAGGCATCATGCAGAAGGTGGCTGGGGAATGGTACGTCTACAAATTTGTCTGTGACCCGGATTCACTTTTCTCCATGGCC
TTCCCCGACAATCAGCGCCTGTTCCTGAAGGCAGAGTCAGAATGCCCCCCTGCCCCCACACACCTCCCACCTCCCGCCAA
TGAGGAGGACACC

Alignment

ORF - retro_rnor_1500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.64 %
• Parental protein coverage: 79.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  TKIKRELHSP-SSELSSCSHEQALGAKYGEKCLYNYCAYDRKPPSGFKPLTPPATPLSPTHQNSLFPPPQ
          TKIK.ELHSP.SSELSSCSHEQALGAKYGEKCLYNYCAYDRKPP.GFKPLTPPATPL.PTH.NSLFPP..
Retrocopy TKIKPELHSP<SSELSSCSHEQALGAKYGEKCLYNYCAYDRKPPFGFKPLTPPATPLPPTH*NSLFPPLK

Parental  ATLPTSALAPGAGPVQGVGPAP-TPHSLPEPGSQQQTFAVPRPPHQP-LQMPKMMPESQYPSEQRFQRQL
          ATLPTSALAPGA..VQGVGP.P..PHSLPEPGSQQ.TFAVPR.P.QP.LQMPKMMPESQYPSEQRFQRQL
Retrocopy ATLPTSALAPGACSVQGVGPVP<SPHSLPEPGSQQHTFAVPRSPYQP<LQMPKMMPESQYPSEQRFQRQL

Parental  SEPCRPFPPQSGVPGDTRPSYQRQMSEPVVPAAPPPLQGFKQEYHDPLYEHGVPGMPGPPAHGFQSPMGI
          SEPCRPFPPQSGVPGDT.PSYQRQM.E.VVPAA.PPLQGFKQEYH.P.YEHG.PGMPGPPAHGFQSP.GI
Retrocopy SEPCRPFPPQSGVPGDTHPSYQRQMLELVVPAALPPLQGFKQEYHNPHYEHGIPGMPGPPAHGFQSPLGI

Parental  KQEPRDYCADSEV-PNCQSPYMRGRYFSSNHEGFTYE-KDPR--LYFDDTCVVPERLEGKVKQEPTMYRE
          KQ.PRDYCADSEV..NCQSPYMRGRYFSSNHEGFTYE.K.P...LYFDDTCV.PERLEGKVK.EPTMY.E
Retrocopy KQ*PRDYCADSEV<ANCQSPYMRGRYFSSNHEGFTYE<KGPQAILYFDDTCVMPERLEGKVKKEPTMYQE

Parental  GPPYQRRGSLQLWQFLVTLLDDPANAHFIAWTGRGMEFKLIEPEEVARRWGIQKNRPAMNYDKLSRSLRY
          GPPYQR.GSLQLWQFL.TLLDDPANAHFIAWTG...EFKL.EPEEVA.RWGIQKN.PAMNYDKLSRSLRY
Retrocopy GPPYQRQGSLQLWQFLATLLDDPANAHFIAWTGQDVEFKLTEPEEVAGRWGIQKNQPAMNYDKLSRSLRY

Parental  YYEKGIMQKVAGERYVYKFVCDPDALFSMAFPDNQRPFLKAESDCPLNEEDTLPLTHFEDS
          YYEKGIMQKVAGE.YVYKFVCDPD.LFSMAFPDNQR.FLKAES.CP.......P....ED.
Retrocopy YYEKGIMQKVAGEWYVYKFVCDPDSLFSMAFPDNQRLFLKAESECPPAPTHLPPPANEEDT

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	85.41 RPM
SRP017611_kidney	0.00 RPM	28.12 RPM
SRP017611_liver	0.00 RPM	2.76 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1500 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1500 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013420	1 retrocopy	retro_cfam_1414,
Mus musculus	ENSMUSG00000013089	1 retrocopy	retro_mmus_572,
Rattus norvegicus	ENSRNOG00000001785	2 retrocopies	retro_rnor_1500 , retro_rnor_417,
Tarsius syrichta	ENSTSYG00000009845	1 retrocopy	retro_tsyr_2106,