RetrogeneDB ID: retro_rnor_1547

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:162604568..162604945(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000038186
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RGD1305713
• Ensembl ID: ENSRNOG00000019514
• Aliases: None
• Description: UPF0235 protein C15orf40 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q505I4]

Sequence

>retro_rnor_1547
ATGCCTAAGAAAGCTGCTGCAACAAGCAAGCGTAAAAACCAAACCAAGGAACCAGAGACACCACCTCCCCCTACAGGGCC
TGCAGCAACTGATTCTAAAGGCTTTGTCACCATAGCCATCCATGCCAAACCCAGCTCCAAACAGAATGTCGTGACAGATC
TGAACACCGAGGCCGTTGGTGTGGCATCGCGGCACCTCCATCTCAGGGAGAGGCAAATGCAGAGCTCTGTTGGTACCTTT
CCAAGGTCTTGGACCTCAGGAAGAGTGACGTGGCTCTGGATAAGGGCGGTAAATCTCGGGAAAAGGTGGTGAAGCTCTTG
GCCTCTACAACTCCAGAGGAGGTCTTGGAGAAGCTGAGAACAGAAACTGAAAAACAG

Alignment

ORF - retro_rnor_1547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKKAGATSKGKNQTKEPETPPPPTGPVATDSKGFVTIAIHAKPGSKQNAVTDLNTEAVGVA-IAAPPSE
          MPKKA.ATSK.KNQTKEPETPPPPTGP.ATDSKGFVTIAIHAKP.SKQN.VTDLNTEAVGVA.IAAPPS.
Retrocopy MPKKAAATSKRKNQTKEPETPPPPTGPAATDSKGFVTIAIHAKPSSKQNVVTDLNTEAVGVA<IAAPPSQ

Parental  GEANAELCRYLSKVLDLRKSDVVLDKGGKSREKVVKLLASTTPEEVLEKLRTEAEKK
          GEANAELC.YLSKVLDLRKSDV.LDKGGKSREKVVKLLASTTPEEVLEKLRTE.EK.
Retrocopy GEANAELCWYLSKVLDLRKSDVALDKGGKSREKVVKLLASTTPEEVLEKLRTETEKQ

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	6.04 RPM
SRP017611_kidney	0.00 RPM	2.93 RPM
SRP017611_liver	0.00 RPM	2.42 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1547 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1547 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1547 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016522	2 retrocopies	retro_btau_1724, retro_btau_485,
Canis familiaris	ENSCAFG00000013185	2 retrocopies	retro_cfam_39, retro_cfam_420,
Callithrix jacchus	ENSCJAG00000015877	2 retrocopies	retro_cjac_1108, retro_cjac_4086,
Equus caballus	ENSECAG00000022459	1 retrocopy	retro_ecab_374,
Homo sapiens	ENSG00000169609	1 retrocopy	retro_hsap_1881,
Gorilla gorilla	ENSGGOG00000023062	1 retrocopy	retro_ggor_1378,
Microcebus murinus	ENSMICG00000009564	2 retrocopies	retro_mmur_1387, retro_mmur_1601,
Myotis lucifugus	ENSMLUG00000007515	1 retrocopy	retro_mluc_2487,
Macaca mulatta	ENSMMUG00000015890	1 retrocopy	retro_mmul_664,
Monodelphis domestica	ENSMODG00000019374	1 retrocopy	retro_mdom_145,
Nomascus leucogenys	ENSNLEG00000010930	1 retrocopy	retro_nleu_1803,
Oryctolagus cuniculus	ENSOCUG00000005072	1 retrocopy	retro_ocun_211,
Procavia capensis	ENSPCAG00000016446	1 retrocopy	retro_pcap_51,
Pongo abelii	ENSPPYG00000006737	1 retrocopy	retro_pabe_1561,
Rattus norvegicus	ENSRNOG00000019514	2 retrocopies	retro_rnor_1547 , retro_rnor_2334,
Sorex araneus	ENSSARG00000006314	1 retrocopy	retro_sara_147,
Sarcophilus harrisii	ENSSHAG00000017947	2 retrocopies	retro_shar_233, retro_shar_442,
Sus scrofa	ENSSSCG00000030131	1 retrocopy	retro_sscr_221,
Tupaia belangeri	ENSTBEG00000014387	6 retrocopies	retro_tbel_1151, retro_tbel_2000, retro_tbel_3071, retro_tbel_3546, retro_tbel_4182, retro_tbel_4371,