RetrogeneDB ID: retro_rnor_1063

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:74528412..74529173(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cbll1
• Ensembl ID: ENSRNOG00000007253
• Aliases: None
• Description: E3 ubiquitin-protein ligase Hakai [Source:RefSeq peptide;Acc:NP_001101488]

Sequence

>retro_rnor_1063
CACACTGACAATGAGCTACAAGGCGCTAAGAGTTCCGGACCCTTGGGTAGTCTTGATGTTTGCAGAAGAATTCCTATAAA
ACTCGTCTCTAAACAAGCCAACAACATTAAACCTGCACCTCAAACTCAAAGGACTATTAGCAGGATGCCTGAGGCCCACA
AGGTGATGAAGAAGGATTCTAATGAAGAACCATGGTATGATTGTAAAGGGGGCGAATTCCTTCAAATCAGCAAAGATATC
CAAGACACCTTTTTTTTGTGATTTTCAGACAAACATCTTAGGAGAAAAGGACGATCTAGCAGTTCATTTCTGTCACAAAT
GTGGATTGTCTATTAAAGTCTATGGGGAAATGATTTGAAGTAAGCATGTCTTTTGATATGACATGTCCTTTTTACATGAA
AAGGGGAGATAAGAAGTGCCCAAGATGTAGTGATCCTGTGCAGTGAATTGAACAGTGCACGCAAGGTTCTCTCTTCATGT
GTTGCACTGTTCAAGGTTGCAAGAGAATATATCTGTCTCAGAAAGACTTCCAAGCTCATATCAACCATAGCTCTATGAGA
GCTGGAAAGCCTGTTACCTGTGCTTCGCGTGAGAATGTTCATCCTCCTATTGCCTCATCACCAACTCCAATCCCCGATCA
TTTCATAACGTCACCAGACAAGCATCATAAGCGCCATATTCCTCCAAAGCAGCACACAATGCCGCAACCGCCTCCTTTGT
AGCACGAGCACAATAATCAGCCACGTGAGAATATCTGTGCT

Alignment

ORF - retro_rnor_1063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.8 %
• Parental protein coverage: 52.66 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HTDNELQGTNSSGSLGGLDVRRRIPIKLISKQANKVKPAPRTQRTVSRMPAKAAQEGFDYNEEQRYDCK-
          HTDNELQG..SSG.LG.LDV.RRIPIKL.SKQAN..KPAP.TQRT.SRMP........D.NEE..YDCK.
Retrocopy HTDNELQGAKSSGPLGSLDVCRRIPIKLVSKQANNIKPAPQTQRTISRMPEAHKVMKKDSNEEPWYDCK>

Parental  GGELFGNQRRFPGHLFWDFKINILGEKDDTPVHFCDKCGLPIKVYGRMIPCKHVFCYD-CAILHEKKGDK
          G...F............DF..NILGEKDD..VHFC.KCGL.IKVYG.MI..KHVF.YD.C.....K.GDK
Retrocopy GANSFKSAKISKTXXXXDFQTNILGEKDDLAVHFCHKCGLSIKVYGEMI*SKHVF*YD>CPF-YMKRGDK

Parental  MCPGCSDPVQRIEQCTRGSLFMCSIVQGCKRTYLSQRDLQAHINHRHMRAGKPVTRASLENVHPPIAPPP
          .CP.CSDPVQ.IEQCT.GSLFMC..VQGCKR.YLSQ.D.QAHINH..MRAGKPVT.AS.ENVHPPIA..P
Retrocopy KCPRCSDPVQ*IEQCTQGSLFMCCTVQGCKRIYLSQKDFQAHINHSSMRAGKPVTCASRENVHPPIASSP

Parental  TEIPDRFIMPPDKHHMSHIPPKQHIMMPPPPLQHVPHEHYNQPHEDIRA
          T.IPD.FI..PDKHH..HIPPKQH.M..PPPL.H...EH.NQP.E.I.A
Retrocopy TPIPDHFITSPDKHHKRHIPPKQHTMPQPPPL*H---EHNNQPRENICA

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	29.19 RPM
SRP017611_kidney	0.00 RPM	19.82 RPM
SRP017611_liver	0.00 RPM	13.31 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1063 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1063 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1063 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016379	1 retrocopy	retro_cjac_4046,
Homo sapiens	ENSG00000105879	1 retrocopy	retro_hsap_49,
Gorilla gorilla	ENSGGOG00000004921	1 retrocopy	retro_ggor_164,
Microcebus murinus	ENSMICG00000012936	1 retrocopy	retro_mmur_1635,
Nomascus leucogenys	ENSNLEG00000008660	1 retrocopy	retro_nleu_19,
Pongo abelii	ENSPPYG00000017904	1 retrocopy	retro_pabe_112,
Pan troglodytes	ENSPTRG00000019583	1 retrocopy	retro_ptro_67,
Rattus norvegicus	ENSRNOG00000007253	1 retrocopy	retro_rnor_1063 ,