RetrogeneDB ID: retro_rnor_2747

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:100891942..100892449(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000015579
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Casp3
• Ensembl ID: ENSRNOG00000010475
• Aliases: Casp3, Lice
• Description: Caspase-3 Caspase-3 subunit p17 Caspase-3 subunit p12 [Source:UniProtKB/Swiss-Prot;Acc:P55213]

Sequence

>retro_rnor_2747
TCACAGCAAAAGGAGCAGTTGTGTGTGTGTGATTCTAAGCCATGGCGGCGAAAGGTTTTTGGAACGAATGGACCTATTGA
CCTGAAAAAACTAACTAGTTTCTTCAGAGACAACTACTACTGGAGTCTGAGTGGAAAACCAAAACTCTTCATCATTCAGA
CCTGCCGTTGTACTGAACTGTACTGTGGCATTGAGACAGACAGTGGAACTGACAATGATATGGCATGCCCGAAGATACCA
GTGGAGGCCAACTTCCTGCATGCTTACTCTACAGCACCTGGTTATTATTCCTGGAGAAATTCAAAGGAATGTTCATGGTT
CATTCAGTCACTTTGTGCCATGCTGAAACTGTGCGCGCACAAGTTGGAATTCATGCACATCCTTACCCGTGTTAACTGGA
AGGTGGCCACGGAATTTAAGTCATTCTCCCTGGACGCCACTTTCCACGCAAAGAATCAGATCCCATGTATTGTGTCAATG
CTCACAAAAGAACTGTACTTTTATCAC

Alignment

ORF - retro_rnor_2747 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.29 %
• Parental protein coverage: 61.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKRSSFVCVILSHGDEGVIFGTNGPVDLKKLTSFFRGDYCRSLTGKPKLFIIQACRGTELDCGIETDSGT
          S......CV..S.......FGTNGP.DLKKLTSFFR..Y..SL.GKPKLFIIQ.CR.TEL.CGIETDSGT
Retrocopy SQQKEQLCVCDSKPWRRKVFGTNGPIDLKKLTSFFRDNYYWSLSGKPKLFIIQTCRCTELYCGIETDSGT

Parental  DDDMACQKIPVEADFLYAYSTAPGYYSWRNSRDGSWFIQSLCAMLKLYAHKLEFMHILTRVNRKVATEFE
          D.DMAC.KIPVEA.FL.AYSTAPGYYSWRNS...SWFIQSLCAMLKL.AHKLEFMHILTRVN.KVATEF.
Retrocopy DNDMACPKIPVEANFLHAYSTAPGYYSWRNSKECSWFIQSLCAMLKLCAHKLEFMHILTRVNWKVATEFK

Parental  SFSLDATFHAKKQIPCIVSMLTKELYFYH
          SFSLDATFHAK.QIPCIVSMLTKELYFYH
Retrocopy SFSLDATFHAKNQIPCIVSMLTKELYFYH

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	16.32 RPM
SRP017611_kidney	0.00 RPM	13.19 RPM
SRP017611_liver	0.00 RPM	21.38 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2747 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2747 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2747 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005740	2 retrocopies	retro_cjac_2678, retro_cjac_3011,
Cavia porcellus	ENSCPOG00000012511	2 retrocopies	retro_cpor_1203, retro_cpor_1450,
Dasypus novemcinctus	ENSDNOG00000013931	1 retrocopy	retro_dnov_1013,
Dipodomys ordii	ENSDORG00000002554	2 retrocopies	retro_dord_178, retro_dord_620,
Homo sapiens	ENSG00000164305	1 retrocopy	retro_hsap_406,
Gorilla gorilla	ENSGGOG00000025155	1 retrocopy	retro_ggor_402,
Microcebus murinus	ENSMICG00000004809	2 retrocopies	retro_mmur_1389, retro_mmur_691,
Macaca mulatta	ENSMMUG00000012053	1 retrocopy	retro_mmul_114,
Nomascus leucogenys	ENSNLEG00000010895	1 retrocopy	retro_nleu_1005,
Otolemur garnettii	ENSOGAG00000005985	2 retrocopies	retro_ogar_1756, retro_ogar_3263,
Pongo abelii	ENSPPYG00000015236	1 retrocopy	retro_pabe_312,
Pan troglodytes	ENSPTRG00000016640	1 retrocopy	retro_ptro_310,
Rattus norvegicus	ENSRNOG00000010475	1 retrocopy	retro_rnor_2747 ,
Sarcophilus harrisii	ENSSHAG00000009178	1 retrocopy	retro_shar_404,
Ictidomys tridecemlineatus	ENSSTOG00000003865	2 retrocopies	retro_itri_172, retro_itri_586,