RetrogeneDB ID: retro_rnor_110

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:227413057..227413663(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000050510
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rab1
• Ensembl ID: ENSRNOG00000004992
• Aliases: None
• Description: RAB1, member RAS oncogene family [Source:MGI Symbol;Acc:MGI:97842]

Sequence

>retro_rnor_110
ATGAACCCCGAATATGACTACCTGTTTAAGCTGCTTTTGATTGGTGACTCGGGCGTGGGCAAGTCATGCCTGCTTCTGCG
GTTTGCTGATGACACGTACACAGAGAGCTACATCAGCACCATTGGGGTGGACTTCAAGATTCGAACCATTGAACTGGATG
GCAAAACCATCAAACTACAGATTTGGGACACAGCTGGTCAGGAACGGTTCAGGACCATCACTTCCAGCTACTATCGGGGT
GCTCATGGCATCATTGTGGTGTATGACGTCACTGACCAGGAATCCTACGCTAATGTGAAACAGTGGCTGCAGGAAATAGA
TCGCTACGCCAGTGAGAATGTCAATAAACTGCTGGTAGGCAACAAGAGTGACCTCACCACCAAGAAGGTCGTGGACAATA
CCACAGCCAAGGAATTTGCAGACTCTCTGGGTGTCCCCTTCCTGGAGACAAGTGCCAAGAATGCCACCAATGTTGAACAG
GCATTCATGACAATGGCTGCAGAGATCAAAAAACGGATGGGGCCAGGAGCAGCATCTGGGGGTGAACGGCCCAACCTGAA
GATCGACAGCACTCCTGTGAAATCTGCTAGTGGTGGCTGCTGCTAG

Alignment

ORF - retro_rnor_110 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.07 %
• Parental protein coverage: 56. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNV
          DDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQES..NV
Retrocopy DDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESYANV

Parental  KQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEI
          KQWLQEIDRYASENVNKLLVGNK.DLTTKKVVD.TTAKEFADSLG.PFLETSAKNATNVEQ.FMTMAAEI
Retrocopy KQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAKEFADSLGVPFLETSAKNATNVEQAFMTMAAEI

Parental  KKRMGPGATAGGAEKSNVKIQSTPVKQS
          KKRMGPGA..GG.E..N.KI.STPVK..
Retrocopy KKRMGPGAASGG-ERPNLKIDSTPVKSA

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	18.05 RPM	100.65 RPM
SRP017611_kidney	27.28 RPM	155.41 RPM
SRP017611_liver	9.41 RPM	68.72 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_110 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_110 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_110 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
Dipodomys ordii	ENSDORG00000002112	1 retrocopy	retro_dord_305,
Echinops telfairi	ENSETEG00000002205	2 retrocopies	retro_etel_1687, retro_etel_413,
Homo sapiens	ENSG00000138069	2 retrocopies	retro_hsap_2362, retro_hsap_3626,
Macaca mulatta	ENSMMUG00000021721	1 retrocopy	retro_mmul_951,
Oryctolagus cuniculus	ENSOCUG00000017003	1 retrocopy	retro_ocun_800,
Pongo abelii	ENSPPYG00000012360	1 retrocopy	retro_pabe_2135,
Pan troglodytes	ENSPTRG00000011989	1 retrocopy	retro_ptro_1727,
Rattus norvegicus	ENSRNOG00000004992	1 retrocopy	retro_rnor_110 ,
Rattus norvegicus	ENSRNOG00000019295	1 retrocopy	retro_rnor_455,
Ictidomys tridecemlineatus	ENSSTOG00000020693	1 retrocopy	retro_itri_1541,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,