RetrogeneDB ID: retro_pabe_1959

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:68636333..68636885(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHORDC1
• Ensembl ID: ENSPPYG00000003764
• Aliases: CHORDC1, CHP-1
• Description: cysteine and histidine-rich domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001125118]

Sequence

>retro_pabe_1959
GATGAAATTAAGATTGGGACCTCATGTAAGAATGGAGGGTGTTCAAAGACATATCAGGGTCTAGAGAGTCTAGAAGAAGT
CTGTGTGTATCATTCTGGAGTACCTATTTTCCATGAGGGGATGAAATACTGGAGCTGTTGTAGAAGAAAAACTTCTGATT
TTAATACATTCTTAGCCCAAGAGGGCTGTTCAACAGGGAAACACATATGGGCTGAAAAGGATGCTGGGGAAAATGTTGTT
CCATGTAGAGATGACTGGCATCAGACTGAAGGTGAAGTTACCATTTCAGTATATGCTAAAAATTCACTTCCAGAACTTAG
TCGAGTAGAAGTAAATAGCACGTTGTTAAATGTGCACATTGGATTTGAAGGAGAGAAAGAATTTGATCAAAATATGAAAT
TATGGGGTGTGACTGATGTAAAGTGAAGTTATGTAACTATGACTGCAACAAAGATTGAGATCACTATGAGAAAAGCTGAA
CCAATGCAGAGGGCAAGCCTTGAACTGCCTGCAGCCAAAAAGCAGGAAAAACAAAAAGACAACACAACAGAT

Alignment

ORF - retro_pabe_1959 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.76 %
• Parental protein coverage: 55.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DEIKIGTSCKNGGCSKTYRGLESLEEVCVYHSGVPIFHEGMKYWSCCRRKTSDFNTFLAQEGCTKGKHMW
          DEIKIGTSCKNGGCSKTY.GLESLEEVCVYHSGVPIFHEGMKYWSCCRRKTSDFNTFLAQEGC..GKH.W
Retrocopy DEIKIGTSCKNGGCSKTYQGLESLEEVCVYHSGVPIFHEGMKYWSCCRRKTSDFNTFLAQEGCSTGKHIW

Parental  TKKDAGKKVVPCRHDWHQTGGEVTISVYAKNSLPELSRVEANSTLLNVHIVFEGEKEFDQNVKLWGVIDV
          ..KDAG..VVPCR.DWHQT.GEVTISVYAKNSLPELSRVE.NSTLLNVHI.FEGEKEFDQN.KLWGV.DV
Retrocopy AEKDAGENVVPCRDDWHQTEGEVTISVYAKNSLPELSRVEVNSTLLNVHIGFEGEKEFDQNMKLWGVTDV

Parental  KRSYVTMTATKIEITMRKAEPMQWASLELPAAKKQEKQKDDTTD
          K.SYVTMTATKIEITMRKAEPMQ.ASLELPAAKKQEKQKD.TTD
Retrocopy K*SYVTMTATKIEITMRKAEPMQRASLELPAAKKQEKQKDNTTD

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	0.06 RPM	15.59 RPM
SRP007412_cerebellum	0.00 RPM	15.20 RPM
SRP007412_heart	0.00 RPM	16.50 RPM
SRP007412_kidney	0.03 RPM	10.57 RPM
SRP007412_liver	0.00 RPM	9.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1959 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1959 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1959 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2252
Pan troglodytes	retro_ptro_1595
Gorilla gorilla	retro_ggor_1679
Macaca mulatta	retro_mmul_1024

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000903	4 retrocopies	retro_cjac_2220, retro_cjac_2927, retro_cjac_4147, retro_cjac_815,
Echinops telfairi	ENSETEG00000013104	2 retrocopies	retro_etel_1713, retro_etel_1860,
Felis catus	ENSFCAG00000019389	1 retrocopy	retro_fcat_137,
Homo sapiens	ENSG00000110172	3 retrocopies	retro_hsap_1452, retro_hsap_1903, retro_hsap_2252,
Gorilla gorilla	ENSGGOG00000027396	3 retrocopies	retro_ggor_1117, retro_ggor_1118, retro_ggor_1679,
Loxodonta africana	ENSLAFG00000017340	1 retrocopy	retro_lafr_401,
Macaca mulatta	ENSMMUG00000005209	2 retrocopies	retro_mmul_1024, retro_mmul_1923,
Nomascus leucogenys	ENSNLEG00000007079	5 retrocopies	retro_nleu_1085, retro_nleu_1232, retro_nleu_1320, retro_nleu_752, retro_nleu_981,
Oryctolagus cuniculus	ENSOCUG00000014147	1 retrocopy	retro_ocun_1595,
Otolemur garnettii	ENSOGAG00000003523	1 retrocopy	retro_ogar_2724,
Pongo abelii	ENSPPYG00000003764	5 retrocopies	retro_pabe_1199, retro_pabe_1554, retro_pabe_1734, retro_pabe_1959 , retro_pabe_461,
Pan troglodytes	ENSPTRG00000004164	3 retrocopies	retro_ptro_1253, retro_ptro_1595, retro_ptro_988,
Tupaia belangeri	ENSTBEG00000002910	1 retrocopy	retro_tbel_2891,
Tarsius syrichta	ENSTSYG00000004205	1 retrocopy	retro_tsyr_1581,