RetrogeneDB ID: retro_rnor_1109

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:53874285..53875132(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000045880
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSRNOG00000048441
• Aliases: None
• Description: None

Sequence

>retro_rnor_1109
AATGGCGAGACGTCATCTCCAGTAGCGATGATGACTCCATCATGCTCTATTACTGCCAGGAGGGCAAACCAAAGAGAACC
CTGTACAGTAAGAAATATGGTGTGGAACTCATCAGATATACCCATGCAGCAAACACAGTCGTTTATAGCTCTAACAAAAT
AGATGATACTATTTGTTACTTGTCCTTGCATGACAATAAATACATCAGACACTTTCCTGGACACAGCAAGAGGGTGGTGG
CCTTGTCCATGTCACCTGTGGATGACACTTTGATTTCTGGGTCTCTTGATAAGACCATTCAACTCTGGGATCTCCGGTCT
CCTAACTGCCAGGGCCTCATGCATCTACAGGGCAAACCCATTTGTCCTTTGATCCAGAAGGGTTAATTTTTGCTGCAGGT
GTCAACTCAGAAATGGTCAAACTTTATGACCTTCGTTCTTTTGATAAGGGTCCATTTGCTACCTTTAAGAGGCAGTATGA
TCGGACTTGTGAGTGGACAGGAATTAAGTTCAGCAATGGTGGCAAACTGATACTCATCTCCACCAACTGCAGCTTCATCT
GCCTCATTGACGCATTTAAGGGTGTGGTGGTGATGCACACATATGGGAGTTATGCTAATAGCAAAGCTGTTACACTCAAA
TCTTCGTTTAATCCAGATTCACAGTTTATTATGATTGGTTAAGAAGATGGCAAAATACATGTGTGGAATGGGGAGAGTGG
TATAAAAGTAGCTGTACTGGATGGGAAACACAGCGGCCCCATCACCTGTTTGCAGTTCAACCCCAAGTTTATGGCCTTTG
CCAGTGCCTGTTCCAACATGGCCTTCTGGTTACGCACCATTGATGAC

Alignment

ORF - retro_rnor_1109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.16 %
• Parental protein coverage: 90.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NGET-VISSSDDDSIVLYDCQEGKWMMVVISCAFGLFRARDTQAAESLVFSKVKMQHTIRYLSLHDNKYI
          NGET.VISSSDDDSI.LY.CQEGK......S...G....R.T.AA...V.S..K...TI.YLSLHDNKYI
Retrocopy NGET<VISSSDDDSIMLYYCQEGKPKRTLYSKKYGVELIRYTHAANTVVYSSNKIDDTICYLSLHDNKYI

Parental  RYFPGHSKRVVALSMSPVDDTFISGSLDKTIRLWDLRSPNCQGLMHLQGKPVC-SFDPEGLIFAAGVNSE
          R.FPGHSKRVVALSMSPVDDT.ISGSLDKTI.LWDLRSPNCQGLMHLQGKP.C.SFDPEGLIFAAGVNSE
Retrocopy RHFPGHSKRVVALSMSPVDDTLISGSLDKTIQLWDLRSPNCQGLMHLQGKPIC<SFDPEGLIFAAGVNSE

Parental  MVKLYDLRSFDKGPFATFKMQYDRTCEWTGLKFSNDGKLILISTNGSFIRLIDAFKG-VVMHTFGGYANS
          MVKLYDLRSFDKGPFATFK.QYDRTCEWTG.KFSN.GKLILISTN.SFI.LIDAFKG.VVMHT.G.YANS
Retrocopy MVKLYDLRSFDKGPFATFKRQYDRTCEWTGIKFSNGGKLILISTNCSFICLIDAFKGVVVMHTYGSYANS

Parental  KAVTLEASFTPDSQFIMIGSEDGKIHVWNGESGIKVAVLDGKHTGPITCLQFNPKFMTFASACSNMAFWL
          KAVTL..SF.PDSQFIMIG.EDGKIHVWNGESGIKVAVLDGKH.GPITCLQFNPKFM.FASACSNMAFWL
Retrocopy KAVTLKSSFNPDSQFIMIG*EDGKIHVWNGESGIKVAVLDGKHSGPITCLQFNPKFMAFASACSNMAFWL

Parental  PTIDD
          .TIDD
Retrocopy RTIDD

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	0.07 RPM	26.53 RPM
SRP017611_kidney	0.07 RPM	16.96 RPM
SRP017611_liver	0.00 RPM	11.70 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1109 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1109 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1109 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000774	1 retrocopy	retro_chof_2299,
Callithrix jacchus	ENSCJAG00000006114	1 retrocopy	retro_cjac_3022,
Homo sapiens	ENSG00000164091	2 retrocopies	retro_hsap_2816, retro_hsap_419,
Loxodonta africana	ENSLAFG00000028309	1 retrocopy	retro_lafr_639,
Macropus eugenii	ENSMEUG00000009280	1 retrocopy	retro_meug_1207,
Macaca mulatta	ENSMMUG00000008234	2 retrocopies	retro_mmul_339, retro_mmul_511,
Monodelphis domestica	ENSMODG00000011614	4 retrocopies	retro_mdom_1259, retro_mdom_144, retro_mdom_219, retro_mdom_398,
Nomascus leucogenys	ENSNLEG00000007104	2 retrocopies	retro_nleu_1016, retro_nleu_1195,
Otolemur garnettii	ENSOGAG00000016032	1 retrocopy	retro_ogar_1314,
Pongo abelii	ENSPPYG00000013812	2 retrocopies	retro_pabe_185, retro_pabe_300,
Rattus norvegicus	ENSRNOG00000048441	3 retrocopies	retro_rnor_1003, retro_rnor_1109 , retro_rnor_1152,