RetrogeneDB ID: retro_rnor_1926

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:147361504..147362055(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Bcl2l12
• Ensembl ID: ENSRNOG00000020486
• Aliases: None
• Description: bcl-2-like protein 12 [Source:RefSeq peptide;Acc:NP_001101950]

Sequence

>retro_rnor_1926
ATGGCCGACTCTGAAGAGTTGGGTCTCCAAGAGGACACACTGAAGGTTCTGACTGCCTTCCTTAGGTGCAGTGAAGCTGC
TGGGTCCCCTATCCCAACTCCACCCAAGAACCCTGCCCAAGAAGAGACAACAGATTTCCTGAGCTTCCCCTAAAGATGCC
TCCCTTGTCCCCTGGGAAGAGGAGGTCCTTCCCTTGGGTCCTCTAGGCCCTGCTGCCTTCCCCTCCGCCACTGTTATGGT
TCGGAGCCTGGCCCAGCCACTCCAGACTTCTATGCCCTGGTTGCCCAGCGTCTGGAACAGCTGGTACAGAAGCAACTCAA
GTCTCCGCCCACCTCAAAGATTCAGGGACCCCCCCTCCCACGGAGAAGGAAGCCCTGCTAAGCAGGCTGGTAGCCTTGAT
GGAGGAGGAGGCGGAAGTCATCAACCAAAAGCTGGCATCTGACCCAGCTCTGCATCATAAACTGGCCCTCCTGTCAGAAG
GCTCTTTCGCCCACCTTGTGGAACTCTTCTCTAGCCCGAGGGGCAGCTCCTCCCCAAACTGCTCAAGCCCC

Alignment

ORF - retro_rnor_1926 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.08 %
• Parental protein coverage: 71.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGSEELGLQEDTLKVLTAFLRRGETAGSPVPTPPRSPAQEETTDFLSRLRRCLPCPLGREAPPPESSRP
          MA.SEELGLQEDTLKVLTAFLR..E.AGSP.PTPP..PAQEETTDFLS...RCLPCPLGR..P...SSRP
Retrocopy MADSEELGLQEDTLKVLTAFLRCSEAAGSPIPTPPKNPAQEETTDFLSFP*RCLPCPLGRGGPSLGSSRP

Parental  CFLPLRPCYGSEPGPASSDFYALVAQRLEQLVQEQLKSPPSSEIQGPP-PTEK-EALLRRLVALLEEEAE
          C.LPLR.CYGSEPGPA..DFYALVAQRLEQLVQ.QLKSPP.S.IQGPP.P....EALL.RLVAL.EEEAE
Retrocopy CCLPLRHCYGSEPGPATPDFYALVAQRLEQLVQKQLKSPPTSKIQGPPLPRRR<EALLSRLVALMEEEAE

Parental  VINQKLASDPALHRKLARLSAGSFARLVELFSSRGGSSSPNCSSP
          VINQKLASDPALH.KLA.LS.GSFA.LVELFSS..GSSSPNCSSP
Retrocopy VINQKLASDPALHHKLALLSEGSFAHLVELFSSPRGSSSPNCSSP

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	0.86 RPM
SRP017611_kidney	0.00 RPM	2.65 RPM
SRP017611_liver	0.00 RPM	1.82 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1926 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1926 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1926 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000003926	1 retrocopy	retro_mmul_1196,
Rattus norvegicus	ENSRNOG00000020486	2 retrocopies	retro_rnor_1926 , retro_rnor_726,