RetrogeneDB ID: retro_rnor_796

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:41983554..41984028(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lrrc57
• Ensembl ID: ENSRNOG00000009143
• Aliases: None
• Description: leucine-rich repeat-containing protein 57 [Source:RefSeq peptide;Acc:NP_001012354]

Sequence

>retro_rnor_796
ATGGGAAACAGTGCCTTCCATTCTCATATGGAAACAGCGCAGAAAACCGGTGTCTGTCAGCTTAAAGACCATGATCTGAC
TGAGTTCCCCTTAGAGTTGCAGAAGCTGATGAGCAATCTTAGGACCATCAATTTGTCCAACAAAATTGACAGTCTACCAC
CTCTGATAATAGGAAAGTTCACTCTTCTAAAGAGCCTATCCCTCAACCTCAAACTGACTGTTCTACCTGCTGAACTAGGC
AATCTGAAAAAACTAGAGACACTAAGTCTCAACAACGATCCCCTGAGAGAGCTACCGTCTACCTCTGGGCAGCTGTTGGC
ACTGAAGACCCTGAGCATCTCTGGGAATTAGCTGGGAGCATTACCACCCCAGCTTTGTAGCATGTGACATCTGGTTATAG
CAGATCTCTCCAAAAACCAGATTCAGAGTATACTTGACACAGTCGGGGAGCTGCAGGCCTTTGAACTCGATCTC

Alignment

ORF - retro_rnor_796 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.62 %
• Parental protein coverage: 97.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNSALRAHVETAQKTGVFQLKDRGLTEFPSELQKLTSNLRTIDLSNNKIDSLPPLIIGKFTLLKSLSLN
          MGNSA...H.ETAQKTGV.QLKD..LTEFP.ELQKL.SNLRTI.LSN.KIDSLPPLIIGKFTLLKSLSLN
Retrocopy MGNSAFHSHMETAQKTGVCQLKDHDLTEFPLELQKLMSNLRTINLSN-KIDSLPPLIIGKFTLLKSLSLN

Parental  NNKLTVLPDELCNLKKLETLSLNNNHLRELPSSFGQLSALKTLSLSGNQLGALPPQLCSLRHLDVVDLSK
          ..KLTVLP.EL.NLKKLETLSLNN..LRELPS..GQL.ALKTLS.SGN.LGALPPQLCS..HL...DLSK
Retrocopy L-KLTVLPAELGNLKKLETLSLNNDPLRELPSTSGQLLALKTLSISGN*LGALPPQLCSM*HLVIADLSK

Parental  NQIRSIPDTVGELQAIELNL
          NQI.SI.DTVGELQA.EL.L
Retrocopy NQIQSILDTVGELQAFELDL

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	17.40 RPM
SRP017611_kidney	0.00 RPM	10.12 RPM
SRP017611_liver	0.00 RPM	3.43 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_796 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_796 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_796 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006482	1 retrocopy	retro_chof_2306,
Callithrix jacchus	ENSCJAG00000002991	1 retrocopy	retro_cjac_2819,
Homo sapiens	ENSG00000180979	1 retrocopy	retro_hsap_2163,
Gorilla gorilla	ENSGGOG00000009597	1 retrocopy	retro_ggor_1718,
Loxodonta africana	ENSLAFG00000005465	2 retrocopies	retro_lafr_1027, retro_lafr_767,
Macaca mulatta	ENSMMUG00000001544	1 retrocopy	retro_mmul_901,
Nomascus leucogenys	ENSNLEG00000004485	1 retrocopy	retro_nleu_1812,
Otolemur garnettii	ENSOGAG00000007751	1 retrocopy	retro_ogar_3437,
Pan troglodytes	ENSPTRG00000006976	2 retrocopies	retro_ptro_1649, retro_ptro_1650,
Rattus norvegicus	ENSRNOG00000009143	1 retrocopy	retro_rnor_796 ,
Rattus norvegicus	ENSRNOG00000048310	1 retrocopy	retro_rnor_1732,