RetrogeneDB ID: retro_pabe_2749

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:73080212..73080650(-)
• Located in intron of: ENSPPYG00000015546

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHP
• Ensembl ID: ENSPPYG00000006370
• Aliases: CHP1, CHP
• Description: calcium-binding protein p22 [Source:RefSeq peptide;Acc:NP_001127537]

Sequence

>retro_pabe_2749
GATTTCCTGAGGATTCCAGAACTTGTCATCAACCCACTGGAGGACTGAATCATCAATGCCTTCTTTCCAGAGGGAGAGGA
CCAGGTAAACTTCCGTGGATTCATGTGAACTTTGGCTCATTTCCACCCCATTGAGGATAATGAAAAGAGCAAAGATGTGA
ATGGACCCGAACCACTCAACAGCCAAAGCAACAAACTGCAGTTTGCTTTTCGACTATATAATTTCGATAAAGATGATAAG
CTCTCCCGTGGTGAACTGATACAGGTGCTACGCTTAATGGTCAGAGTAAATATCTCAGATGAGCAGCTTGGCTGCATCGC
AGACAGGACCATTCAAGAGGCTGATCAGGATGGGGACAGTGCCATATATTTCACAGAATTTGTTAAGGTTTTGGAGAAGG
TAGATGTAGAACAGAAAATGAGCATCTAATTTCTTCAC

Alignment

ORF - retro_pabe_2749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.99 %
• Parental protein coverage: 74.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFQRIPELAINPLGDRIINAFFPEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAF
          DF.RIPEL.INPL.D.IINAFFPEGEDQVNFRGFM.TLAHF.PIEDNEKSKDVNGPEPLNS.SNKL.FAF
Retrocopy DFLRIPELVINPLED*IINAFFPEGEDQVNFRGFM*TLAHFHPIEDNEKSKDVNGPEPLNSQSNKLQFAF

Parental  RLYDLDKDEKISRDELLQVLRMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKM
          RLY..DKD.K.SR.EL.QVLR.MV.VNISDEQLG.IADRTIQEADQDGDSAI.FTEFVKVLEKVDVEQKM
Retrocopy RLYNFDKDDKLSRGELIQVLRLMVRVNISDEQLGCIADRTIQEADQDGDSAIYFTEFVKVLEKVDVEQKM

Parental  SIRFLH
          SI.FLH
Retrocopy SI*FLH

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	0.00 RPM	48.16 RPM
SRP007412_cerebellum	0.00 RPM	16.29 RPM
SRP007412_heart	0.00 RPM	12.64 RPM
SRP007412_kidney	0.03 RPM	28.97 RPM
SRP007412_liver	0.09 RPM	15.55 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2749 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2749 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2749 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3334
Pan troglodytes	retro_ptro_2144
Gorilla gorilla	retro_ggor_1293
Macaca mulatta	retro_mmul_2088

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027173	1 retrocopy	retro_btau_1785,
Canis familiaris	ENSCAFG00000009525	1 retrocopy	retro_cfam_2136,
Callithrix jacchus	ENSCJAG00000020761	1 retrocopy	retro_cjac_2396,
Cavia porcellus	ENSCPOG00000010577	2 retrocopies	retro_cpor_1224, retro_cpor_726,
Equus caballus	ENSECAG00000019751	1 retrocopy	retro_ecab_1099,
Felis catus	ENSFCAG00000006346	1 retrocopy	retro_fcat_1964,
Homo sapiens	ENSG00000187446	2 retrocopies	retro_hsap_3334, retro_hsap_3541,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Loxodonta africana	ENSLAFG00000014743	3 retrocopies	retro_lafr_221, retro_lafr_795, retro_lafr_838,
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,
Oryctolagus cuniculus	ENSOCUG00000013832	1 retrocopy	retro_ocun_68,
Otolemur garnettii	ENSOGAG00000013099	2 retrocopies	retro_ogar_2442, retro_ogar_628,
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,
Pteropus vampyrus	ENSPVAG00000003150	1 retrocopy	retro_pvam_1207,
Rattus norvegicus	ENSRNOG00000004742	2 retrocopies	retro_rnor_2034, retro_rnor_2223,
Ictidomys tridecemlineatus	ENSSTOG00000014503	1 retrocopy	retro_itri_227,