RetrogeneDB ID: retro_ptro_1253

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:13723797..13724782(+)
• Located in intron of: ENSPTRG00000009833

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHORDC1
• Ensembl ID: ENSPTRG00000004164
• Aliases: None
• Description: Pan troglodytes cysteine and histidine-rich domain (CHORD) containing 1 (CHORDC1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246422]

Sequence

>retro_ptro_1253
GCCTTGCTGTGCTACAACCGGAGCTGCGGTCAGCGCTTCGATCCTGAGACCAATTCCGACGATGCTTGCACATATCACCC
AGGTGTTCCAGTCTTTCACGATGCATTAAAGGGTTGGTCTTGCTGTAAGAGAAGAACAACTGATTTTTCTGATTTCTTAA
GCATTGTAGGCTGTACAAAAGGTAGACATAATAGTGAGAAGCCACCTGAGCCAGTCAAACCTGAAGTCAAGACTACTGAG
AAGAAGGAACTATCTGAATTAAAACCAAAATTTCAGGAACACATTCAAGCCCCTAAGACAATAGACGCGATAAAAAGACC
AAGCCCAGATGAACCAATGACAAATTTGGAATTAAAAATATCTGCCTCCCTAAAACAAGCACTTGATAAACTTAAACTGT
TATCAGGGAATGAAGAAAATAAGAAAAGAAGACAATGATGAAATTAAGATTGGGACCTCATGTAAGAATGGAGGGTGTTC
AAAGACATATCGGGGTCTAAAGAGTCTAGAAGAAGTCTGTGTATATCATTCTGGAGTACCTGTTTTCCATGAGGGGACGA
AATACTGGAGCTGTTGTAGAAGAAAAACTTCTGATTTTAATACATTCTTAGACCAAGAGGGCTGTACAAAAGAGAAACAT
GTGGACTAAAAAAGATGCTGGGAAAAAAGTTGTTCCATGTAGACATGACTGGCATCAGACTGGAGGTGAAGTTACCATTT
CCGTATAGGCTAAAAATTCACTTCCAGAGCTTAGTCGAGTAGAAGCAAATAGCACATTGTTAGATGCGCATATTGTATTT
GAAGGAGAGAAGGAATTTGATCAAAATGTGAAATTATAGGGTGTGATTGATGTAAAGCGAAGTTATTAACTATGACTGCA
ACAAAGATTGAAATCACTATGAGAAAAGCTGAACCGATGCAGTGGGCAAGCCTTGAACTGTCTGCAGCTAAAAAGCAGGA
AAAACAAAAAGACGACACAGCAGAT

Alignment

ORF - retro_ptro_1253 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.75 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ALLCYNRGCGQRFDPETNSDDACTYHPGVPVFHDALKGWSCCKRRTTDFSDFLSIVGCTKGRHNSEKPPE
          ALLCYNR.CGQRFDPETNSDDACTYHPGVPVFHDALKGWSCCKRRTTDFSDFLSIVGCTKGRHNSEKPPE
Retrocopy ALLCYNRSCGQRFDPETNSDDACTYHPGVPVFHDALKGWSCCKRRTTDFSDFLSIVGCTKGRHNSEKPPE

Parental  PVKPEVKTTEKKELSELKPKFQEHIIQAPKPVEAIKRPSPDEPMTNLELKISASLKQALDKLKLSSGNEE
          PVKPEVKTTEKKELSELKPKFQEHI.QAPK...AIKRPSPDEPMTNLELKISASLKQALDKLKL.SGNEE
Retrocopy PVKPEVKTTEKKELSELKPKFQEHI-QAPKTIDAIKRPSPDEPMTNLELKISASLKQALDKLKLLSGNEE

Parental  NK-KEEDNDEIKIGTSCKNGGCSKTYQGLESLEEVCVYHSGVPIFHEGMKYWSCCRRKTSDFNTFLAQEG
          NK.KE...DEIKIGTSCKNGGCSKTY.GL.SLEEVCVYHSGVP.FHEG.KYWSCCRRKTSDFNTFL.QEG
Retrocopy NK>KEDN-DEIKIGTSCKNGGCSKTYRGLKSLEEVCVYHSGVPVFHEGTKYWSCCRRKTSDFNTFLDQEG

Parental  CTKGKHM-WTKKDAGK-KVVPCRHDWHQTGGEVTISVYAKNSLPELSRVEANSTLLNVHIVFEGEKEFDQ
          CTK.KH....KK..GK.KVVPCRHDWHQTGGEVTISV.AKNSLPELSRVEANSTLL..HIVFEGEKEFDQ
Retrocopy CTKEKHV<GLKKMLGK<KVVPCRHDWHQTGGEVTISV*AKNSLPELSRVEANSTLLDAHIVFEGEKEFDQ

Parental  NVKLWGVIDVKRSY-VTMTATKIEITMRKAEPMQWASLELPAAKKQEKQKDDTTD
          NVKL.GVIDVKRSY..TMTATKIEITMRKAEPMQWASLEL.AAKKQEKQKDDT.D
Retrocopy NVKL*GVIDVKRSY<LTMTATKIEITMRKAEPMQWASLELSAAKKQEKQKDDTAD

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	0.11 RPM	19.77 RPM
SRP007412_cerebellum	0.04 RPM	19.18 RPM
SRP007412_heart	0.09 RPM	21.54 RPM
SRP007412_kidney	0.08 RPM	20.35 RPM
SRP007412_liver	0.43 RPM	11.39 RPM
SRP007412_testis	0.11 RPM	47.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1253 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1253 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1253 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1903
Pongo abelii	retro_pabe_1554

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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,