RetrogeneDB ID: retro_rnor_1237

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:59160370..59160878(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000047834
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Sri
• Ensembl ID: ENSRNOG00000049780
• Aliases: None
• Description: sorcin [Source:RefSeq peptide;Acc:NP_001121662]

Sequence

>retro_rnor_1237
TTCCTTGGACAAACTCAGGATCCACTATGTTGTTACTTCGCTGCTGTGGCTGGACAGGATGGACAAATTGATGCTGACCA
GTTGCAGAGATGTCTGACACAGTCTGGCATTGAGGGAGGATGCAAACCTTTTAACCTGGAGACTTGTCTTATGGTTTCAA
TGTTGGATAAACATATGTCTGGCACGATGGGGTTCAATGAATTCAAAGAGCTCTGGGCTGTGCTGAATGGCTGGAGACAA
CACTTCATCAATTTCAATAGTGATAGGAGTGGAACAGTGGATCACCAGGAACTGCAGAAGGCCCTAACCACTATGGGATT
CAGGTTGAGGCCCCAAACGGTGATTTCAGTTGCAAAGCTTGCAACAGCAGTGGGAAGACCGCCTTTGGTGACTACATTGC
CTACTGCGTCCAACTGAGGGCTCTCACAGCTTTCGAAGACGGGATTCTGGTCAACAAAAAGTTGTGAATTTCTCATATGA
TGACTTCATCCAGTGTGTCATGACCGTT

Alignment

ORF - retro_rnor_1237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.01 %
• Parental protein coverage: 86.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FPGHTQDPLYGYFAAVAGQDGQIDADELQRCLTQSGIAGGYKPFNLETCRLMVSMLDRDMSGTMGFSEFR
          F.G.TQDPL..YFAAVAGQDGQIDAD.LQRCLTQSGI.GG.KPFNLETC.LMVSMLD..MSGTMGF.EF.
Retrocopy FLGQTQDPLCCYFAAVAGQDGQIDADQLQRCLTQSGIEGGCKPFNLETC-LMVSMLDKHMSGTMGFNEFK

Parental  ELWTVLSGWRQHFISFDSDRSGTVDPQELQKALTTMGFRLSPQTVNSVA-KRYSTSGKITFDDYIACCVK
          ELW.VL.GWRQHFI.F.SDRSGTVD.QELQKALTTMGFRL.PQTV.SVA.K....SGK..F.DYIA.CV.
Retrocopy ELWAVLNGWRQHFINFNSDRSGTVDHQELQKALTTMGFRLRPQTVISVA<KACNSSGKTAFGDYIAYCVQ

Parental  LRALT-DSFRRRDSGQQGVVNFSYDDFIQCVMTV
          LRALT....RR....Q..V.NFSYDDFIQCVMTV
Retrocopy LRALT<SFRRRDSGQQKVV-NFSYDDFIQCVMTV

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	32.86 RPM
SRP017611_kidney	0.00 RPM	63.64 RPM
SRP017611_liver	0.00 RPM	14.46 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1237 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1237 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1237 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001855	1 retrocopy	retro_cfam_498,
Cavia porcellus	ENSCPOG00000010096	1 retrocopy	retro_cpor_216,
Latimeria chalumnae	ENSLACG00000000210	1 retrocopy	retro_lcha_89,
Loxodonta africana	ENSLAFG00000027380	2 retrocopies	retro_lafr_1186, retro_lafr_487,
Monodelphis domestica	ENSMODG00000010355	1 retrocopy	retro_mdom_782,
Mustela putorius furo	ENSMPUG00000018313	1 retrocopy	retro_mputfur_1147,
Pteropus vampyrus	ENSPVAG00000007438	2 retrocopies	retro_pvam_1112, retro_pvam_734,
Rattus norvegicus	ENSRNOG00000013972	2 retrocopies	retro_rnor_1563, retro_rnor_2505,
Rattus norvegicus	ENSRNOG00000014485	1 retrocopy	retro_rnor_2840,
Rattus norvegicus	ENSRNOG00000049780	1 retrocopy	retro_rnor_1237 ,
Ictidomys tridecemlineatus	ENSSTOG00000004372	1 retrocopy	retro_itri_607,
Tupaia belangeri	ENSTBEG00000004434	1 retrocopy	retro_tbel_4493,
Tarsius syrichta	ENSTSYG00000014640	1 retrocopy	retro_tsyr_1832,
Xenopus tropicalis	ENSXETG00000008793	1 retrocopy	retro_xtro_25,