RetrogeneDB ID: retro_rnor_2994

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:146551960..146553193(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Suv39h1
• Ensembl ID: ENSRNOG00000039576
• Aliases: Suv39h1, RGD1565028
• Description: histone-lysine N-methyltransferase SUV39H1 [Source:RefSeq peptide;Acc:NP_001100426]

Sequence

>retro_rnor_2994
ACCTCAGGTTGCAGTGTGTGCTGTAAATCTTCCTGGAATCAGCTGCAGGATCTGTGCCGACTAGCCAAGCTTTCTTGTCC
TGCCCTTGGTGTTTCTAAGAAGAATGTGTATGACTTTGAAGTTGAATTCCTGTGTGATTATAAGAAGATCCGTGAGCAGG
AGTATTACCTGGTTAAATGGCGTGGGTATCCCGACTCAGAGAACACGTGGGAGCCACGGCACAATCTCAAATGTGTGCGC
ATTCTTAAAAAGTTCCACAAGGACTTAGAAAGAGAGCTTGTCCGGTGACACCGCCTGCCAAAGCCACCCAGGCATCTGTA
CCCAAACTTAGCCAATTACCTGGTGCAGAAGGCCAAGCAGAGGCGGGCACTGCACCGTTGGGAACAAGAGCTCAATGCCA
AGCGCAGCCACCTGGGGCGGATCACCGTGGAGAATGAGGTAGACCTGGATGGCCCTCCTAGGTCCTTTGTCTATATCAAT
GAGTATCGAGTTGGTGAGGGCATCACCCTCAACCAGGTAGCTGTTGGCTACCTGGACTGTCTGTTGGCACCCACTGGAGG
CTGTTGCCCTGGAGCATCCCTGCACACGTTTGCTTACAATGACCAAGGCCAGGTGCGACTGAAAGCTGGGCAGCCCATCT
ACGAGGGCAACTCTCGCTGTTGCTGTGGCTATGACTGCCCAAACCGTGTAGTCCAGAAAGGCATCGGCTACAACCTCTGC
ATCTTCCGCACTGATGATGGCCGAGGCTGGGGTGTCCGCACGCTGGAAAAGATCCGCAAAAATAGCTTTGTTATGGAGTA
TGTGGGAGAGATTATTACCTCAGAGGAGGCAGAGAGGAGGGGCCAGATCTACGACCGCCAGGGCGCCACCTACCTCTTTG
ACCTGGACTACGTGGAGGACCTATATACCATGGATGCCTGGTGCATCCATGGATCCTATTATGGCAACATCTCTCATTTT
GTCAACCATAGTTGTGATCCCAACCTGCAAGTGTACAACATATTCATAGACAACCTTGACGAGCGACTACCCCGCATCGC
ATTCTTTGCCACAAGAACCATCTGGGCGGGCAAGGAGCTCACCTTTGATTACAACATGCAAGTGGACCCCATGGACATGG
AGAGTACCCGAATGGACTCCAACTTTGGCCTGGCAGGGCTCCCCGACTCCCCCAAGAAACGGGTCCGTATTGAATGCAAA
TGTGGGACAACAGCTTGCCGAAAATACCTCTTC

Alignment

ORF - retro_rnor_2994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.8 %
• Parental protein coverage: 98.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLGCSVCCKSSWNQLQDLCRLAKLSCPALGVSKKNLYDFEVEYLCDYKKIREQEYYLVKWRGYPDSENTW
          T.GCSVCCKSSWNQLQDLCRLAKLSCPALGVSKKN.YDFEVE.LCDYKKIREQEYYLVKWRGYPDSENTW
Retrocopy TSGCSVCCKSSWNQLQDLCRLAKLSCPALGVSKKNVYDFEVEFLCDYKKIREQEYYLVKWRGYPDSENTW

Parental  EPRQNLKCVRILKQFHKDLERELVRRHRRSKPPRHLDPNLANYLVQKAKQRRALQRWEQELNAKRSHLGR
          EPR.NLKCVRILK.FHKDLERELVR.HR..KPPRHL.PNLANYLVQKAKQRRAL.RWEQELNAKRSHLGR
Retrocopy EPRHNLKCVRILKKFHKDLERELVR*HRLPKPPRHLYPNLANYLVQKAKQRRALHRWEQELNAKRSHLGR

Parental  ITVENEVDLDGPPRSFVYINEYRVGEGITLNQVAVGCECQDCLLAPTGGCCPGASLHKFAYNDQGQVRLK
          ITVENEVDLDGPPRSFVYINEYRVGEGITLNQVAVG....DCLLAPTGGCCPGASLH.FAYNDQGQVRLK
Retrocopy ITVENEVDLDGPPRSFVYINEYRVGEGITLNQVAVG--YLDCLLAPTGGCCPGASLHTFAYNDQGQVRLK

Parental  AGQPIYECNSRCCCGYDCPNRVVQKGIRYNLCIFRTDDGRGWGVRTLEKIRKNSFVMEYVGEIITSEEAE
          AGQPIYE.NSRCCCGYDCPNRVVQKGI.YNLCIFRTDDGRGWGVRTLEKIRKNSFVMEYVGEIITSEEAE
Retrocopy AGQPIYEGNSRCCCGYDCPNRVVQKGIGYNLCIFRTDDGRGWGVRTLEKIRKNSFVMEYVGEIITSEEAE

Parental  RRGQIYDRQGATYLFDLDYVEDVYTVDA-AYYGNISHFVNH----SCDPNLQVYNVFIDNLDERLPRIAF
          RRGQIYDRQGATYLFDLDYVED.YT.DA....G.......H....SCDPNLQVYN.FIDNLDERLPRIAF
Retrocopy RRGQIYDRQGATYLFDLDYVEDLYTMDAWCIHGSYYGNISHFVNHSCDPNLQVYNIFIDNLDERLPRIAF

Parental  FATRTIWAGEELTFDYNMQVDPVDMESTRMDSNFGLAGLPGSPKKRVRIECKCGTTACRKYLF
          FATRTIWAG.ELTFDYNMQVDP.DMESTRMDSNFGLAGLP.SPKKRVRIECKCGTTACRKYLF
Retrocopy FATRTIWAGKELTFDYNMQVDPMDMESTRMDSNFGLAGLPDSPKKRVRIECKCGTTACRKYLF

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	9.63 RPM
SRP017611_kidney	0.00 RPM	7.40 RPM
SRP017611_liver	0.00 RPM	2.42 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2994 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2994 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2994 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000039576	1 retrocopy	retro_rnor_2994 ,