RetrogeneDB ID: retro_pabe_1554

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:29616653..29617633(+)
• Located in intron of: ENSPPYG00000009036

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_1554
ATGGCCTTGCTGTGCTACAACTGGAGCTGTGGTCAGTGCTTCGATCCTGAGACCAATTCCGACGATGCTTGCACGTATCA
CCCAGGTGTTCGAGTCTTTCACGATGCATTCAAGGGTTGGTCTTGCTGTAAGAGAAGAACAACTGATTTTTCTGATTTCT
TAAGCATTGTAGGCTGTACAAAAGGTAGACATAATAGTGAGAAGCCACCTGAGCCAGTCAAACCTGAAGTCAAGACTACT
GAGAAGGAACTATCTGAATTAAAACCCAAATTTCAGGAACACATTCAAACCTGTAAGACAGTAGAAGCGATAAAAAGACC
AAGCCCAGATGAACCAATGACAAATTTGGAATTAAAAATATCTGCCTCCCTGAAACAAGCACTTGATAAACTGTCGTCAG
GGAATGAAGAAAAAAAGAAGAAGACAATGATGAAATTAAGATTGGGACCTTATGTAAGAATGGAGGGTGTTCAAAGACAT
ATCGGGGTCTAGAGAGTCTAGAAGAAGTCTGTGTATATCATTCTGGAGTACCTATTTTCCATGAGGGGATGAAATACTGG
AGCTGTTGTAGAAGAAAAACTTTTGATTTTAATACATTCTTAGACCAAGAGGGCTGTACAAAAGGGAAACACATGTGGAC
TAAAAAAGATGCTGGGAAAAAAGTTGTTCCATGTAGACATGACTGGCATCAGACTGGAGGTGAAGTTACCATTTCTGTAT
AAGCTAAAAATTCACTTCCAGAACTTAGTCGAGTAGGAGCAAATAGCACATTGTTAGATGCGCATATTGTATTTGAAGGA
GAGAAAGAATTTGATCAAAATGTGAAATTATGGGGCGTGATTGATGTAAAGCGAAGTTATGTAACTATGACTGCAACAAA
GATTGAAATCACTATGAGAAAAGCTGAACCGATGCAGCGGGCAAGCCTTGAACTGCCTGCAGCCAAAAAGCAGGAAAAAC
AAAAAGACGACACAACAGAT

Alignment

ORF - retro_pabe_1554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.19 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALLCYNRGCGQRFDPETNSDDACTYHPGVPVFHDALKGWSCCKRRTTDFSDFLSIVGCTKGRHNSEKPP
          MALLCYN..CGQ.FDPETNSDDACTYHPGV.VFHDA.KGWSCCKRRTTDFSDFLSIVGCTKGRHNSEKPP
Retrocopy MALLCYNWSCGQCFDPETNSDDACTYHPGVRVFHDAFKGWSCCKRRTTDFSDFLSIVGCTKGRHNSEKPP

Parental  EPVKPEVKTTEKKELSELKPKFQEHIIQAPKPVEAIKRPSPDEPMTNLELKISASLKQALDKLKLSSGNE
          EPVKPEVKTTEK.ELSELKPKFQEH.IQ..K.VEAIKRPSPDEPMTNLELKISASLKQALD..KLSSGNE
Retrocopy EPVKPEVKTTEK-ELSELKPKFQEH-IQTCKTVEAIKRPSPDEPMTNLELKISASLKQALD--KLSSGNE

Parental  ENKK-EEDNDEIKIGTSCKNGGCSKTYRGLESLEEVCVYHSGVPIFHEGMKYWSCCRRKTSDFNTFLAQE
          E.KK.E....EIKIGT.CKNGGCSKTYRGLESLEEVCVYHSGVPIFHEGMKYWSCCRRKT.DFNTFL.QE
Retrocopy EKKK<EDND-EIKIGTLCKNGGCSKTYRGLESLEEVCVYHSGVPIFHEGMKYWSCCRRKTFDFNTFLDQE

Parental  GCTKGKHMWTKKDAGKKVVPCRHDWHQTGGEVTISVYAKNSLPELSRVEANSTLLNVHIVFEGEKEFDQN
          GCTKGKHMWTKKDAGKKVVPCRHDWHQTGGEVTISV.AKNSLPELSRV.ANSTLL..HIVFEGEKEFDQN
Retrocopy GCTKGKHMWTKKDAGKKVVPCRHDWHQTGGEVTISV*AKNSLPELSRVGANSTLLDAHIVFEGEKEFDQN

Parental  VKLWGVIDVKRSYVTMTATKIEITMRKAEPMQWASLELPAAKKQEKQKDDTTD
          VKLWGVIDVKRSYVTMTATKIEITMRKAEPMQ.ASLELPAAKKQEKQKDDTTD
Retrocopy VKLWGVIDVKRSYVTMTATKIEITMRKAEPMQRASLELPAAKKQEKQKDDTTD

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	0.17 RPM	15.59 RPM
SRP007412_cerebellum	0.00 RPM	15.20 RPM
SRP007412_heart	0.18 RPM	16.50 RPM
SRP007412_kidney	0.27 RPM	10.57 RPM
SRP007412_liver	2.05 RPM	9.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1554 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1554 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1554 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1903
Pan troglodytes	retro_ptro_1253

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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,