RetrogeneDB ID: retro_ptro_988

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:89234090..89234739(-)
• Located in intron of: None

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_988
TACAGCTGGGGCTGCGGTCAGCGCTTCGATCATGAGACCGATTCCGATGATGCCTGTACATACCACCCAGGTGTTCCAGT
CTTTCACGATGCTTTAAAGGGTTGGTCTTGCTATAAGAGAAGAACAACTGATTTTTCTGATTTCTTAAGCATTGTAGGCT
GCACAAAAGGTAGACATAATAGTGAGAAGCCACCTGAACCAGTCAAACCTGAAGTCAAGACTACTGAGAAGAAGGAAATA
TCTGAATTGAAACCCAAATTTCAGGAACACATCATTCAAGCCCCTAAGCCAGTAGAAGCAATAAAACGGCCAAGCCCAGA
TGAACCAATGACAAATTTGGAATTAAAAATATCTGCCTCCCCAAAACAAGCACTTGATAAACTGTCGTCAGGGAATGAAG
AAGATAAGAAAGAAGACAATGAAGAAATTAAGATTGGCACCTCATGTAAGAATGGAGGGTGTTCAAAGACGTATCAGGGT
CTAGAGAGTCTAGAAAAGGTTTGAGTATATCATTCTGGAGAAGCTATTTTCCGTGAGGGTATGAAATACTGGAGCTGTTG
TAGAAGAAAAACTTCTGATTTTAGTACATTCTTAGCCCAAGAGGGGCTGTACAACAGGGGAACACATGCGGACTAAAAAG
GATGCTGGG

Alignment

ORF - retro_ptro_988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 65.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YNRGCGQRFDPETNSDDACTYHPGVPVFHDALKGWSCCKRRTTDFSDFLSIVGCTKGRHNSEKPPEPVKP
          Y..GCGQRFD.ET.SDDACTYHPGVPVFHDALKGWSC.KRRTTDFSDFLSIVGCTKGRHNSEKPPEPVKP
Retrocopy YSWGCGQRFDHETDSDDACTYHPGVPVFHDALKGWSCYKRRTTDFSDFLSIVGCTKGRHNSEKPPEPVKP

Parental  EVKTTEKKELSELKPKFQEHIIQAPKPVEAIKRPSPDEPMTNLELKISASLKQALDKLKLSSGNEENKKE
          EVKTTEKKE.SELKPKFQEHIIQAPKPVEAIKRPSPDEPMTNLELKISAS.KQALD..KLSSGNEE.KK.
Retrocopy EVKTTEKKEISELKPKFQEHIIQAPKPVEAIKRPSPDEPMTNLELKISASPKQALD--KLSSGNEEDKK-

Parental  EDNDEIKIGTSCKNGGCSKTYQGLESLEEVCVYHSGVPIFHEGMKYWSCCRRKTSDFNTFLAQE-GCTKG
          EDN.EIKIGTSCKNGGCSKTYQGLESLE.V.VYHSG..IF.EGMKYWSCCRRKTSDF.TFLAQE.GCT.G
Retrocopy EDNEEIKIGTSCKNGGCSKTYQGLESLEKV*VYHSGEAIFREGMKYWSCCRRKTSDFSTFLAQE>GCTTG

Parental  KHMWTKKDAG
          .HM.TKKDAG
Retrocopy EHMRTKKDAG

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	0.07 RPM	19.77 RPM
SRP007412_cerebellum	0.00 RPM	19.18 RPM
SRP007412_heart	0.00 RPM	21.54 RPM
SRP007412_kidney	0.13 RPM	20.35 RPM
SRP007412_liver	0.03 RPM	11.39 RPM
SRP007412_testis	0.21 RPM	47.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_988 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_988 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_988 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1452
Gorilla gorilla	retro_ggor_1117
Pongo abelii	retro_pabe_1199
Callithrix jacchus	retro_cjac_815

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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,