RetrogeneDB ID: retro_ptro_2144

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:42584822..42585402(+)
• Located in intron of: ENSPTRG00000016973

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHP1
• Ensembl ID: ENSPTRG00000006942
• Aliases: None
• Description: calcineurin-like EF-hand protein 1 [Source:HGNC Symbol;Acc:17433]

Sequence

>retro_ptro_2144
ATGGGTTCTCAGCCCTCCATGTTACTGTGGGATGAAGAGCTCGAGGAGATAAAGAAGATCAGTTTTTCCCACAGTCAAAT
CACTTGCTCTACAGCCGGTTCACCAGCCTGGACAAAGGAGAGATGGCATTCTCAGCCATGAAGATTTCCTGAGGATTCCA
GAACTTGTCATCAACCCACTGGGGGACCGAATCATCAATGTCTTCTTTCCAGAGGGAGAGGACCAGGTAAACTTCCATGG
ATTCATGTGAACTTTGGCTCATTTCCACCCCATTGAGGATAATGAAAAGAGCAAAGATGTGAATGGACCCGAACCACTCA
ACAGCCGAAGCAACAAACTGCAGTTTGCTTTTCGACTATATGATTTCGATAAAGATGATAAGCTCTCCCATGGTGAGCTG
ATACAGGTGCTACGCTTAATGGTCAGAGTAAATATCTCAGATGAGCAGCTCGGCAGCATCGCAGACAGGACCATTCAAGA
GGCTGATCAGGATGGGGACAGTGCCATATCTCTCACAGAATTTGTTAAGGTTTTGGAGAAGGTGGATGTAGAACAGAAAA
TGAGCATCCAATTTCTTCAC

Alignment

ORF - retro_ptro_2144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGSRASTLLRDEELEEIKKETGFSHSQIT-RLYSRFTSLDKGE-NGTLSREDFQRIPELAINPLGDRIIN
          MGS..S.LL.DEELEEIKK...FSHSQIT..LYSRFTSLDKGE..G.LS.EDF.RIPEL.INPLGDRIIN
Retrocopy MGSQPSMLLWDEELEEIKK-ISFSHSQIT<LLYSRFTSLDKGE<DGILSHEDFLRIPELVINPLGDRIIN

Parental  AFFPEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDEKISRDELLQV
          .FFPEGEDQVNF.GFM.TLAHF.PIEDNEKSKDVNGPEPLNSRSNKL.FAFRLYD.DKD.K.S..EL.QV
Retrocopy VFFPEGEDQVNFHGFM*TLAHFHPIEDNEKSKDVNGPEPLNSRSNKLQFAFRLYDFDKDDKLSHGELIQV

Parental  LRMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFLH
          LR.MV.VNISDEQLGSIADRTIQEADQDGDSAIS.TEFVKVLEKVDVEQKMSI.FLH
Retrocopy LRLMVRVNISDEQLGSIADRTIQEADQDGDSAISLTEFVKVLEKVDVEQKMSIQFLH

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
SRP007412_brain_prefrontal_cortex	0.04 RPM	119.15 RPM
SRP007412_cerebellum	0.07 RPM	74.35 RPM
SRP007412_heart	0.06 RPM	49.81 RPM
SRP007412_kidney	0.00 RPM	157.04 RPM
SRP007412_liver	0.00 RPM	228.39 RPM
SRP007412_testis	0.00 RPM	17.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2144 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2144 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3334
Gorilla gorilla	retro_ggor_1293
Pongo abelii	retro_pabe_2749
Macaca mulatta	retro_mmul_2088

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009525	1 retrocopy	retro_cfam_2136,
Cavia porcellus	ENSCPOG00000010577	2 retrocopies	retro_cpor_1224, retro_cpor_726,
Homo sapiens	ENSG00000187446	2 retrocopies	retro_hsap_3334, retro_hsap_3541,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Macaca mulatta	ENSMMUG00000017092	2 retrocopies	retro_mmul_1809, retro_mmul_2088,
Mus musculus	ENSMUSG00000014077	4 retrocopies	retro_mmus_1458, retro_mmus_2094, retro_mmus_3133, retro_mmus_3469,
Nomascus leucogenys	ENSNLEG00000003465	4 retrocopies	retro_nleu_1678, retro_nleu_2269, retro_nleu_2608, retro_nleu_2609,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pan troglodytes	ENSPTRG00000006942	2 retrocopies	retro_ptro_2144 , retro_ptro_2407,
Pan troglodytes	ENSPTRG00000041941	1 retrocopy	retro_ptro_2909,
Rattus norvegicus	ENSRNOG00000004742	2 retrocopies	retro_rnor_2034, retro_rnor_2223,
Ictidomys tridecemlineatus	ENSSTOG00000014503	1 retrocopy	retro_itri_227,