RetrogeneDB ID: retro_rnor_380

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:13770871..13771627(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000042797
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RGD1561557
• Ensembl ID: ENSRNOG00000001218
• Aliases: None
• Description: None

Sequence

>retro_rnor_380
ATGGCTGCCTCTACCTTGTCCATTTGCTCCAGTGACTTGAGCTATGACAGCCGGGTCTGCCTGCCCGGTTCCTGTGACTC
TTGCACTGACTCCTCCTGGCAAGTGGACGACTGCCCAGAGAGCTGCTGTGAGCCCTGTGGCTGTGCCCCCAGCTGCTGCC
AGCCTAGCTGCTGTGTTCCTTGCTGTGCCCCCAGTTGCTGTGTCCCCAGCTGTTGCCAGGCCAGCTGCTGTGCCCCCTGC
CTGACTCTCATCTGCACCCCAGTGAGCTGTGTGTCCAGCCCCTGCTGCCAGTCTTCCTCCTGCACACCCTCATGCTGCCA
GCAGTCTAGCTGCCAGCCAGCTTGCTGTACCTGCTCCCCCTGCCAGCAGCCCTGTGGTGTGACCCTTTGCTGCAAGCCTG
TCTGCTGCACACCCATCTGCTCTGAATCCTGCTGCCAGCAGTCTAGCTGCCAGTCCTCCTGCTGCCAGCCCTCCTGCTGT
GTGCCTGTCTGCTGCAGGCCTGTGTGCTGCACACCCATCTGCTCTGCCTCCTCCTCCTCCTGCTGCCAGCCCTCCTGCTG
TGCTCCTGTGTGCTGCAAGCCTGTGTGCTGCAAGCCCTGCTCCAGCCTGTCCCTGCTGTGCAGCCCTGTGTGCAGACCTG
CCTGCTGTGTGCCCACCTCCTCCTGCTGTGCCTCCTCTTGCCAGCCCAGCTGCTGTCGCCCAGCCTCCTGTGTGTCCCTG
CTGTGCCGCCCTGCCTGCTCCAGACAGGCCTGCTGA

Alignment

ORF - retro_rnor_380 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.45 %
• Parental protein coverage: 93.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DARTNSSWQVDDCPESCCEPCGCAPSCCQPSCCVPSCCQSSCCAPSCCAPTCCAPTPCLLCTPVNCVSSP
          D..T.SSWQVDDCPESCCEPCGCAPSCCQPSCCVP.CC..SCC.PSCC...CCAP...L.CTPV.CVSSP
Retrocopy DSCTDSSWQVDDCPESCCEPCGCAPSCCQPSCCVP-CCAPSCCVPSCCQASCCAPCLTLICTPVSCVSSP

Parental  CCQSSCCTPSCCQQSSCQPACCTCSPCQQPCGVTLCCKPVCCVPVCCGASSSCCQQSSCEPSCCTSSPCQ
          CCQSS.CTPSCCQQSSCQPA...C..C..PC....C....CC.PVCC......C..S.C..S.C.SS.CQ
Retrocopy CCQSSSCTPSCCQQSSCQPA---CCTCS-PCQQP-CGVTLCCKPVCC---TPICSESCCQQSSCQSSCCQ

Parental  QPCGVTLCCKPVCCTPICSASSSSCCQPSCCAPVCCKPVCCKPCSSLSLLCSPVCRPACCVPTSSCCASS
          ..C.V..CC.PVCCTPICSASSSSCCQPSCCAPVCCKPVCCKPCSSLSLLCSPVCRPACCVPTSSCCASS
Retrocopy PSCCVPVCCRPVCCTPICSASSSSCCQPSCCAPVCCKPVCCKPCSSLSLLCSPVCRPACCVPTSSCCASS

Parental  CQPNCCRPASCVSLLCRPACSRQAC
          CQP.CCRPASCVSLLCRPACSRQAC
Retrocopy CQPSCCRPASCVSLLCRPACSRQAC

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_380 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_380 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008415	1 retrocopy	retro_amel_1917,
Otolemur garnettii	ENSOGAG00000034456	1 retrocopy	retro_ogar_2681,
Pongo abelii	ENSPPYG00000011492	3 retrocopies	retro_pabe_14, retro_pabe_15, retro_pabe_16,
Rattus norvegicus	ENSRNOG00000001218	2 retrocopies	retro_rnor_380 , retro_rnor_382,