RetrogeneDB ID: retro_rnor_1220

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:32491155..32491452(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000011395
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pin1
• Ensembl ID: ENSRNOG00000020474
• Aliases: None
• Description: peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 [Source:RefSeq peptide;Acc:NP_001100171]

Sequence

>retro_rnor_1220
AGCCAATCTCGGAGGCCCTCATCCTGGCGACAGGAAAAGATCACCAGGAGCAAAGAGGAGGCCTTGGAGCTGATCAATGG
CTACAGCCAGAAGATTAAGTCAGGAGAGGAGGACTTTGAATCTCTGGCCTCACAGTTCAGTGATTGCAGCTCTGCCAAAG
CTAGGGGAGACCTGGGTGCCCTCAGCAGAGGTCAGATGCAGAAACCATTTGAGGATGCATCGTTTGCTCTACGAACCAGG
GAGATGAGTGGGCGGGTGTTCACCGATTCAGGCATCCATATCATCCTACGCACAGAA

Alignment

ORF - retro_rnor_1220 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.96 %
• Parental protein coverage: 60. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQSRRPSSWRQEKITRSKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPF
          SQSRRPSSWRQEKITRSKEEALELINGY.QKIKSGEEDFESLASQFSDCSSAKARGDLGA.SRGQMQKPF
Retrocopy SQSRRPSSWRQEKITRSKEEALELINGYSQKIKSGEEDFESLASQFSDCSSAKARGDLGALSRGQMQKPF

Parental  EDASFALRTGEMSGPVFTDSGIHIILRTE
          EDASFALRT.EMSG.VFTDSGIHIILRTE
Retrocopy EDASFALRTREMSGRVFTDSGIHIILRTE

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	62.62 RPM
SRP017611_kidney	0.00 RPM	27.01 RPM
SRP017611_liver	0.00 RPM	9.88 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1220 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1220 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1220 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006079	1 retrocopy	retro_cjac_2925,
Homo sapiens	ENSG00000127445	1 retrocopy	retro_hsap_168,
Gorilla gorilla	ENSGGOG00000006008	1 retrocopy	retro_ggor_252,
Microcebus murinus	ENSMICG00000001996	1 retrocopy	retro_mmur_1157,
Mus musculus	ENSMUSG00000032171	1 retrocopy	retro_mmus_2072,
Nomascus leucogenys	ENSNLEG00000011999	1 retrocopy	retro_nleu_980,
Pongo abelii	ENSPPYG00000009537	1 retrocopy	retro_pabe_462,
Pan troglodytes	ENSPTRG00000010452	1 retrocopy	retro_ptro_159,
Rattus norvegicus	ENSRNOG00000020474	1 retrocopy	retro_rnor_1220 ,
Tupaia belangeri	ENSTBEG00000003793	1 retrocopy	retro_tbel_1546,