RetrogeneDB ID: retro_rnor_1003

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:48341921..48342767(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_rnor_1003
AATGGCGAGACGGTCATCTCCAGTAGTGATGATGACTCCATCGTGCTATATGACTGCCAGGAGGGCAAACCAAAGAGAAC
CCTGTACAGTAAGAAATATGGTGTGGACCTCATCAGATACACCCATGCAGCAAACACAGTCGTTTACAGCTCTAACTAAA
TAGACGATACTATTCGTTACTTGTTCTTGCATGACAATAAATACATCAGATACTTTCCTGGACACAGCAAGAGGGTGGTG
GCCTTGTACATATCACCTGTGGATGACACTTTCATTTCTGGGTCTCTTGATAAGACCATTCAACTCTGGGATCTCCGGTC
TCCTAACTGCCAGGGTCTCATGCATCTACAGGGCAAACCCGTCTGTTCCTTTGATCCAGAAGGGTTAATTTTTGCTGTAG
GTATCGACTCAGAAATGGTCAAACTTTATGACCTTTGTTCTTTTGATAAGGGTCCATTTGCTACCTTTAAGATGCAATAT
GATCGGACTTGTGAGTGGACAGGACTTAAGTTCAGCAACGTTGGCAAACTGATACTCATCTCCACCAATGGCAGCTTCAT
CCGCCTCATTGACGCATTTAAGGGTGTGGTGATGCACACATTTGGGGGTTATGCTAATAGGAAAGCTGTTACACTCAAAG
CTTCGTTTACTCCAGATTCACAGTTTATTATGATTGGTTCAGAAGATGGCAAATTCCATGTGTGGAATGGGGAGAGTGGT
ATAAAAGTAGCTGTACTGGATGGGAAGCACTCTGGCCCCATCACCTGTTTGCAGTTCAACCCCAAGTTTATGACCTTTGC
CAGCGCCTGTTCCAACATGGCCTTCTGGTTACCCACCATTGATGAC

Alignment

ORF - retro_rnor_1003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.52 %
• Parental protein coverage: 90.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NGETVISSSDDDSIVLYDCQEGKWMMVVISCAFGLFRARDTQAAESLVFSKVKMQHTIRYLSLHDNKYIR
          NGETVISSSDDDSIVLYDCQEGK......S...G....R.T.AA...V.S......TIRYL.LHDNKYIR
Retrocopy NGETVISSSDDDSIVLYDCQEGKPKRTLYSKKYGVDLIRYTHAANTVVYSSN*IDDTIRYLFLHDNKYIR

Parental  YFPGHSKRVVALSMSPVDDTFISGSLDKTIRLWDLRSPNCQGLMHLQGKPVCSFDPEGLIFAAGVNSEMV
          YFPGHSKRVVAL..SPVDDTFISGSLDKTI.LWDLRSPNCQGLMHLQGKPVCSFDPEGLIFA.G..SEMV
Retrocopy YFPGHSKRVVALYISPVDDTFISGSLDKTIQLWDLRSPNCQGLMHLQGKPVCSFDPEGLIFAVGIDSEMV

Parental  KLYDLRSFDKGPFATFKMQYDRTCEWTGLKFSNDGKLILISTNGSFIRLIDAFKGVVMHTFGGYANSKAV
          KLYDL.SFDKGPFATFKMQYDRTCEWTGLKFSN.GKLILISTNGSFIRLIDAFKGVVMHTFGGYAN.KAV
Retrocopy KLYDLCSFDKGPFATFKMQYDRTCEWTGLKFSNVGKLILISTNGSFIRLIDAFKGVVMHTFGGYANRKAV

Parental  TLEASFTPDSQFIMIGSEDGKIHVWNGESGIKVAVLDGKHTGPITCLQFNPKFMTFASACSNMAFWLPTI
          TL.ASFTPDSQFIMIGSEDGK.HVWNGESGIKVAVLDGKH.GPITCLQFNPKFMTFASACSNMAFWLPTI
Retrocopy TLKASFTPDSQFIMIGSEDGKFHVWNGESGIKVAVLDGKHSGPITCLQFNPKFMTFASACSNMAFWLPTI

Parental  DD
          DD
Retrocopy DD

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	0.43 RPM	26.53 RPM
SRP017611_kidney	0.14 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_1003 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1003 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1003 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,