RetrogeneDB ID: retro_rnor_1034

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:8235173..8235446(-)
• Located in intron of: ENSRNOG00000002079

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fkbp2
• Ensembl ID: ENSRNOG00000021153
• Aliases: Fkbp2, RGD1560660
• Description: peptidyl-prolyl cis-trans isomerase FKBP2 precursor [Source:RefSeq peptide;Acc:NP_001127900]

Sequence

>retro_rnor_1034
TTGAAAATAAGGCCCACGGGAAAGCTAGAAGATGGGACGGAGTTTGACAGCAGCCTACCACAGAACCAGCCCTTTGTTTT
CTCCTTTGGCACTGGCCAGGTCATCAAGGGCTGGGACCAGGGGCTACTGGGGATGTGTGAAGGGGAAAAGCAGAAGCTAA
TGATGCCGTCTGAGCTGGGGTATGGAAAGCGGGGAGCCCCCCCAAAGATACCGGGTGGAGCAACCCTGGTGTTTGAGGTG
GAGGTGCTCAAGATTGAGAGACGTTCAGAACTG

Alignment

ORF - retro_rnor_1034 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.01 %
• Parental protein coverage: 65.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LHMHYTGKLEDGTEFDSSLPQNQPFVFSLGTGQVIKGWDQGLLGMCEGEKRKLVIPSELGYGERGAPPKI
          L....TGKLEDGTEFDSSLPQNQPFVFS.GTGQVIKGWDQGLLGMCEGEK.KL..PSELGYG.RGAPPKI
Retrocopy LKIRPTGKLEDGTEFDSSLPQNQPFVFSFGTGQVIKGWDQGLLGMCEGEKQKLMMPSELGYGKRGAPPKI

Parental  PGGATLVFEVELLKIERRSEL
          PGGATLVFEVE.LKIERRSEL
Retrocopy PGGATLVFEVEVLKIERRSEL

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	41.56 RPM
SRP017611_kidney	0.00 RPM	33.01 RPM
SRP017611_liver	0.00 RPM	33.28 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1034 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1034 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1034 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000758	1 retrocopy	retro_acar_126,
Bos taurus	ENSBTAG00000013606	3 retrocopies	retro_btau_1418, retro_btau_69, retro_btau_916,
Callithrix jacchus	ENSCJAG00000018124	2 retrocopies	retro_cjac_2030, retro_cjac_3853,
Cavia porcellus	ENSCPOG00000002928	1 retrocopy	retro_cpor_39,
Macaca mulatta	ENSMMUG00000012945	1 retrocopy	retro_mmul_1397,
Rattus norvegicus	ENSRNOG00000009886	1 retrocopy	retro_rnor_49,
Rattus norvegicus	ENSRNOG00000021153	1 retrocopy	retro_rnor_1034 ,