RetrogeneDB ID: retro_rnor_1519

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:110915589..110916219(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Spic
• Ensembl ID: ENSRNOG00000005720
• Aliases: None
• Description: transcription factor Spi-C [Source:RefSeq peptide;Acc:NP_001101550]

Sequence

>retro_rnor_1519
AAACATAGAAATTACATGGCTATCATTAACCCTTATCCTCACATCAGAGGCAATTCTAACTACTGTGGAATGTTACCACC
CACAGACGAACCCCTCTATGACTGGAGAGGTGTAACAAATGGTTCTGCGGACCTGTATTTGGAAGGAAGCTTCCATCAAT
CCCTACAGAACGTAGCTGAAAGTCAGCTGGTACAAGCCCCTTTCTTCCAGGAAAAGGGAGGAAGAGGCAGGAGGAAGCTT
TGGCAATTTGAATACCTTTTCGAATCCCTGTGCAATTCGGAGATGGTGTCTTGTATCCAGTGGGTCGACAAAGCCAAGGG
CATCTTTCAGTTTATATCAAAAAACAAAGAAAAACTCGCTGAACTCGGCGGAAAAGAAAAGGCAACCGGAAACCAATGAC
TTACCAGAAGATGGCCAGAGCCCTGAGGAATTACGCCAGAACTGGGGCGATCACAAAAATCCGGAGAAAGCTGACCTACC
AGTTCAGCAAAGCTGTTCTCCAAAGACTTGCTCCGTCTCACTTTCTGGGGAAAGACCTCTTCTAACTCACAGTATAACCA
GCCTGATTAGGGCTATCTCAATTTAAACCACTGGAATGCAAATTACTATGCTCACGCCAGTTACCAGAGC

Alignment

ORF - retro_rnor_1519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.87 %
• Parental protein coverage: 98.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EHRNYMAIINPYPHIRGNSNYCGMLPPTEEPLYDWRGVTNGSADLYLEGSFHQSLQNVAETQLVQAPFFQ
          .HRNYMAIINPYPHIRGNSNYCGMLPPT.EPLYDWRGVTNGSADLYLEGSFHQSLQNVAE.QLVQAPFFQ
Retrocopy KHRNYMAIINPYPHIRGNSNYCGMLPPTDEPLYDWRGVTNGSADLYLEGSFHQSLQNVAESQLVQAPFFQ

Parental  EKGGRGRRKLRLFEYLFESLCNSEMVSCIQWVDKAKGIFQFISKNKEKLAELWG-KRKGNRKPMTYQKMA
          EKGGRGRRKL..FEYLFESLCNSEMVSCIQWVDKAKGIFQFISKNKEKLAEL.G.KRKGNRKPMTYQKMA
Retrocopy EKGGRGRRKLWQFEYLFESLCNSEMVSCIQWVDKAKGIFQFISKNKEKLAELGG<KRKGNRKPMTYQKMA

Parental  RALRNYARTGEITKIRRKLTYQFSEAVLQRLAPSHFLGKDLF-YSQYKQPDQGYLNLNHWNANYYAHASY
          RALRNYARTG.ITKIRRKLTYQFS.AVLQRLAPSHFLGKDLF..SQY.QPD.GYLNLNHWNANYYAHASY
Retrocopy RALRNYARTGAITKIRRKLTYQFSKAVLQRLAPSHFLGKDLF>NSQYNQPD*GYLNLNHWNANYYAHASY

Parental  QS
          QS
Retrocopy QS

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.13 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1519 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1519 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1519 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009904	2 retrocopies	retro_btau_1281, retro_btau_1837,
Callithrix jacchus	ENSCJAG00000001906	1 retrocopy	retro_cjac_3835,
Dasypus novemcinctus	ENSDNOG00000004496	1 retrocopy	retro_dnov_759,
Equus caballus	ENSECAG00000009614	1 retrocopy	retro_ecab_542,
Echinops telfairi	ENSETEG00000004217	6 retrocopies	retro_etel_1675, retro_etel_2007, retro_etel_2008, retro_etel_593, retro_etel_929, retro_etel_933,
Homo sapiens	ENSG00000166211	4 retrocopies	retro_hsap_1748, retro_hsap_1800, retro_hsap_3135, retro_hsap_864,
Gorilla gorilla	ENSGGOG00000024597	4 retrocopies	retro_ggor_1324, retro_ggor_1362, retro_ggor_2255, retro_ggor_703,
Loxodonta africana	ENSLAFG00000015661	1 retrocopy	retro_lafr_912,
Myotis lucifugus	ENSMLUG00000011052	1 retrocopy	retro_mluc_2169,
Macaca mulatta	ENSMMUG00000020873	1 retrocopy	retro_mmul_1245,
Nomascus leucogenys	ENSNLEG00000006232	1 retrocopy	retro_nleu_53,
Oryctolagus cuniculus	ENSOCUG00000008070	1 retrocopy	retro_ocun_161,
Otolemur garnettii	ENSOGAG00000015148	1 retrocopy	retro_ogar_1782,
Pongo abelii	ENSPPYG00000004873	4 retrocopies	retro_pabe_1444, retro_pabe_1445, retro_pabe_2819, retro_pabe_686,
Pan troglodytes	ENSPTRG00000005351	4 retrocopies	retro_ptro_1206, retro_ptro_1218, retro_ptro_3070, retro_ptro_598,
Rattus norvegicus	ENSRNOG00000005720	1 retrocopy	retro_rnor_1519 ,
Ictidomys tridecemlineatus	ENSSTOG00000015457	3 retrocopies	retro_itri_1785, retro_itri_235, retro_itri_29,
Tursiops truncatus	ENSTTRG00000017205	1 retrocopy	retro_ttru_1708,