RetrogeneDB ID: retro_rnor_2974

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:122205233..122205974(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tes
• Ensembl ID: ENSRNOG00000032978
• Aliases: None
• Description: Testin [Source:UniProtKB/Swiss-Prot;Acc:Q2LAP6]

Sequence

>retro_rnor_2974
AAGGAGATGAGGCAGTTTGTGAAGAAATATAAGAATGAAGCTCTGGGAGTGGGTGACGTGAGGCTTCCCTCTGAGATGAA
TGTTCAACATTACAAGGGGCACAACCCTGCTACAGACAGAAACACCCCAACAGCAGTGGATTTCAAAGACACATCTATGG
AGCCTAAGAAGCCTCAATATTCCTGTTATTCCTGCAAACACGCCGTGAAGGAAGGAAACCCAGCCATCTTTGCTGAAAGG
GCTGGCTATGATAAACTCTGGCACCCGGCTTGCTTTATTTGCACCATCTGTGGTGAAATCCTGGTAGACATGATTTACTT
CTGGAAGAATGGGAAGCTGTATTGTGGCAGACATTACTGTGACAGTGAGAAGCCCCGTTGTGCTGGCTGTGATGAGCTGA
TATTCAGCAATGAATATACCCAAGCAGAAAACAAGAATTGGCATTTGATACACTTTTGCTGCTTTCACTGCCACAATGTC
CTGGCAGGAAAAATATATGTGATGGTTGGATCAAAACCTGTGTGCAAGTCCTGTTACATGAAGATCCATGCTGTGGTGTG
TCAAGGATGCCACAATGCCATAGACCCAGAAGAGCAGAGAGTAATCTACCAAAACTTCAGCTGGCATGCATCCACGGCAT
GCTTCCTGTGCTCCTGTTGCAGCAAGTGTCTTCTTGGGAAGAAGTTCATACGTGTAGAAGGGATGATTTTCTGTTCCATA
GAGTGTAAGAATATGATGTCC

Alignment

ORF - retro_rnor_2974 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.38 %
• Parental protein coverage: 58.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEMEQFVKKYKSEALGVGDVKLPSEMNAQGDKVHNPAGDRNTPAAVGSKDKSAEAKKTQYSCYCCKNTMR
          KEM.QFVKKYK.EALGVGDV.LPSEMN.Q..K.HNPA.DRNTP.AV..KD.S.E.KK.QYSCY.CK....
Retrocopy KEMRQFVKKYKNEALGVGDVRLPSEMNVQHYKGHNPATDRNTPTAVDFKDTSMEPKKPQYSCYSCKHAVK

Parental  EGDPAIYAERAGYDKLWHPACFICSTCGELLVDMIYFWKNGKLYCGRHYCDSEKPRCAGCDELIFSNEYT
          EG.PAI.AERAGYDKLWHPACFIC..CGE.LVDMIYFWKNGKLYCGRHYCDSEKPRCAGCDELIFSNEYT
Retrocopy EGNPAIFAERAGYDKLWHPACFICTICGEILVDMIYFWKNGKLYCGRHYCDSEKPRCAGCDELIFSNEYT

Parental  QAENQNWHLKHFCCFDCDNILAGKIYVMVRDKPVCKPCYVKNHAVVCQGCHNAIDPEVQRVTYNNFSWHA
          QAEN.NWHL.HFCCF.C.N.LAGKIYVMV..KPVCK.CY.K.HAVVCQGCHNAIDPE.QRV.Y.NFSWHA
Retrocopy QAENKNWHLIHFCCFHCHNVLAGKIYVMVGSKPVCKSCYMKIHAVVCQGCHNAIDPEEQRVIYQNFSWHA

Parental  STECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKMMS
          ST.CFLCSCCSKCL.G.KF..VEGM.FCS.ECK.MMS
Retrocopy STACFLCSCCSKCLLGKKFIRVEGMIFCSIECKNMMS

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	8.27 RPM
SRP017611_kidney	0.00 RPM	12.56 RPM
SRP017611_liver	0.00 RPM	1.95 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2974 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2974 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2974 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005193	2 retrocopies	retro_cjac_3361, retro_cjac_3870,
Mus musculus	ENSMUSG00000029552	3 retrocopies	retro_mmus_253, retro_mmus_3438, retro_mmus_3586,
Rattus norvegicus	ENSRNOG00000032978	3 retrocopies	retro_rnor_2974 , retro_rnor_2975, retro_rnor_9,