RetrogeneDB ID: retro_rnor_1304

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:43491970..43492340(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tpi1
• Ensembl ID: ENSRNOG00000015290
• Aliases: Tpi1, Tpi
• Description: Triosephosphate isomerase [Source:UniProtKB/Swiss-Prot;Acc:P48500]

Sequence

>retro_rnor_1304
CTTGGGGTGATGCTCTGTATTGGGGAGAAGCTAGATGAAAGGGAAGCTGGCATCACCAAGACAGTTGTTTTCGAGCAAAC
CTAGTTCACCACAGATAATATGAAAGATAATATGAAAGTCATCATGACCTATGAACAGTATGGGCCATTGGTACTGGCAC
GACTACAACACCTCAAGAGCCCAGGAAGTATATGAGATGCTATGATTAAAATCCAATGTGTGATGTGGTAACTCAGATCA
CCCACATCATTTCTGGAGGTTCTGTGACTGGAGCTACCTGCAAAGGACTGGCAAACTAGCCTGGTGTGGACAGCTTCCTC
CTGGTGGTACACCTCTCAAGCCTGAATTGGTAGATATCACTAATGACAAA

Alignment

ORF - retro_rnor_1304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.04 %
• Parental protein coverage: 51.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDWCKVVLAYEP-VWAIGTGKTATPQQAQEVHEKLR
          LGV..CIGEKLDEREAGIT..VVFEQT................YE..VWAIGTG.T.TP...QE.....R
Retrocopy LGVMLCIGEKLDEREAGITKTVVFEQT*FTXXXXXXXXXXIMTYEQ<VWAIGTGTTTTP---QEPRKYMR

Parental  GWLKCNVSEGVAQCTRIIYGGSVTGATCKELASQPDVDGFLV-GGASLKPEFVDIINAK
          ..........V.Q.T.II.GGSVTGATCK.LA..P.VD.FL..GG..LKPE.VDI.N.K
Retrocopy CYD*NPMCDVVTQITHIISGGSVTGATCKGLAN*PGVDSFLL<GGTPLKPELVDITNDK

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	0.36 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1304 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1304 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1304 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007348	2 retrocopies	retro_cjac_2190, retro_cjac_2370,
Homo sapiens	ENSG00000111669	3 retrocopies	retro_hsap_3038, retro_hsap_3510, retro_hsap_3784,
Gorilla gorilla	ENSGGOG00000002623	1 retrocopy	retro_ggor_151,
Macropus eugenii	ENSMEUG00000006977	5 retrocopies	retro_meug_1348, retro_meug_1520, retro_meug_1934, retro_meug_267, retro_meug_512,
Myotis lucifugus	ENSMLUG00000024989	4 retrocopies	retro_mluc_1090, retro_mluc_1311, retro_mluc_1777, retro_mluc_1807,
Macaca mulatta	ENSMMUG00000005194	2 retrocopies	retro_mmul_1864, retro_mmul_250,
Mustela putorius furo	ENSMPUG00000016774	1 retrocopy	retro_mputfur_136,
Mus musculus	ENSMUSG00000023456	4 retrocopies	retro_mmus_1180, retro_mmus_3260, retro_mmus_532, retro_mmus_558,
Nomascus leucogenys	ENSNLEG00000004821	2 retrocopies	retro_nleu_1120, retro_nleu_847,
Otolemur garnettii	ENSOGAG00000031254	1 retrocopy	retro_ogar_109,
Pongo abelii	ENSPPYG00000004207	1 retrocopy	retro_pabe_2902,
Pan troglodytes	ENSPTRG00000004595	4 retrocopies	retro_ptro_160, retro_ptro_1999, retro_ptro_2382, retro_ptro_2565,
Rattus norvegicus	ENSRNOG00000015290	1 retrocopy	retro_rnor_1304 ,
Rattus norvegicus	ENSRNOG00000050669	2 retrocopies	retro_rnor_2615, retro_rnor_787,