RetrogeneDB ID: retro_ptro_2814

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:22005043..22006427(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KHSRP
• Ensembl ID: ENSPTRG00000010364
• Aliases: None
• Description: KH-type splicing regulatory protein [Source:HGNC Symbol;Acc:6316]

Sequence

>retro_ptro_2814
AAGATCGCAGCCAAAATTGTAGGTGATGCTGCAACGACAGTGAATAACAGCACTCCTGATTTTGGTCTAGGGGGCCATAA
GAGACAGTTGGAAGATGGAGATCAACCGGAGAGCAAGAAGCTGGCTTCCCAGGGAGACTCAATCAGTTCTCAACTTGGAC
CCATCCATCATCCCCCAGGACTTCAATGACAGAAGAGTACAGGGTCCCAGACGGTGTGGTGGGCCTGATCTTTGGCAGAG
GGGGCGAACAAATTGACAAAATCTAACAGGATTCAGCCTGCAAAGTACAGATTACTCCAGGCAGCAGTGGCCTACCCAAG
CACAGTGTGTCCTTGACAAGAGCCCCAGAATCTCTCCAGAAAGCGAAGATGATGCTGGATGACATTGTGTCTCGGGGTCA
TGGGGGGCCCCCAGGACAGTTCCACGACACCGCCAACGGGGGCCAGAATGGCACTGTACAGGACATGATCCCTGCGGGCA
AGGCCGGCCTGGTCATCGCCAAGGGCGGGGAGACCATGAAACAGCTGCAGGAATACGCTGGAGTGAAGATGATCTTAATT
CAAGATGGTTCTCAGAACACGAAGGTGGACAACCCTCTCCGGATCCCTGGGGATCCTTACAAAGTGCAGCAAGCCTGCCA
GATGGTGATGGACATCCTCCGGGAACGTGACCAAGGCGGCTTTGGGGACTGGAATGATTACGGATCTCGGACTGGCGGGG
GCATTGATGTGCCGGTGCCCAGGCATTCTGTCGCCGTGGTCATTGGCCGGAGAGGAGAGATGATCAAGAAGATCCAGAAT
GACGCTGGGGTGCCGATACAGTTCAAGCAAGATGATGGGACAGGGCCCGAGAAGATTGCTCATATAATGGGGTCCCCAGA
CAGGTGCGAGCACGCAGCCCGGATCATCAACGACCTCCTCCAGAGCCTCAGGAGTGGTCCCCCAGGCCCTCCAAGGGGTC
CAGGCATGCCCCCGGGGAGGCCGAGGAAGAGGCCAACGCAACTGGGGGCCCCCTGGCGGGGAGATGACCTTCTCCATCCC
CACTCACAAGCGCCGGCTGGTCATCGGCCGAGGTGGCCAGAACGTGAAAGTCATAAACCAGCAGACTGGAGCCTTCCTAG
AGATCTCCCGGCAGCTACCATCCAGTGGGGATCCCAACTTCAAGTCGTTCATCATCCAGGGTTCGCCCCAGCAGATCCAA
CACGCCGAGCAGCTTATCGAGGGGGCCCTTCAACCAGGGGCCACCTGGGCTCCCCCGCGTGCCGGGGGGCTCCCTCCTTA
CCAGGGCTGGGGCAATACCTACCCACAGTGGCAACCGCCTGCTACTCACGATCCAAGCAAAGCAGCTGCGGCTACCGCGG
GCGCCAACGCCACATGGGCCGCCT

Alignment

ORF - retro_ptro_2814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.09 %
• Parental protein coverage: 64.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QIAAKIGGDAATTVNNSTPDFGFGGQKRQLEDGDQPESKKLASQGDSISSQLGPIHPPP-RTSMTEEYRV
          .IAAKI.GDAATTVNNSTPDFG.GG.KRQLEDGDQPESKKLASQGDSISSQLGPIH.PP.RTSMTEEYRV
Retrocopy KIAAKIVGDAATTVNNSTPDFGLGGHKRQLEDGDQPESKKLASQGDSISSQLGPIHHPP<RTSMTEEYRV

Parental  PDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSRGRGGPPG
          PDG.VGLI.GRGGEQI.KI.QDS.CKVQI.P.S.GLP..SVSLT.APES.QKAKMMLDDIVSRG.GGPPG
Retrocopy PDGVVGLIFGRGGEQIDKI*QDSACKVQITPGSSGLPKHSVSLTRAPESLQKAKMMLDDIVSRGHGGPPG

Parental  QFHDNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYK
          QFHD.ANGGQNGTVQ..MIPAGKAGLVI.KGGET.KQLQE.AGVKMILIQDGSQNT.VD.PLRI.GDPYK
Retrocopy QFHDTANGGQNGTVQD-MIPAGKAGLVIAKGGETMKQLQEYAGVKMILIQDGSQNTKVDNPLRIPGDPYK

Parental  VQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD
          VQQAC.MVMDILRERDQGGFGD.N.YGSR.GGGIDVPVPRHSV.VVIGR.GEMIKKIQNDAGV.IQFKQD
Retrocopy VQQACQMVMDILRERDQGGFGDWNDYGSRTGGGIDVPVPRHSVAVVIGRRGEMIKKIQNDAGVPIQFKQD

Parental  DGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPP-GGRGRGRGQGNWGPPGGEMTFS
          DGTGPEKIAHIMG.PDRCEHAARIINDLLQSLRSGPPGPP.GPGMPP.GGR..GRGQ.NWGPPGGEMTFS
Retrocopy DGTGPEKIAHIMGSPDRCEHAARIINDLLQSLRSGPPGPPRGPGMPP>GGR--GRGQRNWGPPGGEMTFS

Parental  IPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPLC
          IPTHK..LVIGRGG.NVK.INQQTGAF.EISRQLP..GDPNFK.FII.GSPQQI.HA.QLIE........
Retrocopy IPTHKRRLVIGRGGQNVKVINQQTGAFLEISRQLPSSGDPNFKSFIIQGSPQQIQHAEQLIEGALQPGAT

Parental  PVGPGPGGPGPAGPMGPFNP---GPFNQGPPGAPPHAGG-PPPHQYP
          ...P..GG..P....G...P....P....P..A.....G.P.PH..P
Retrocopy WAPPRAGGLPPYQGWGNTYPQWQPPATHDPSKAAAATAG>PTPHGPP

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	49.66 RPM
SRP007412_cerebellum	0.00 RPM	97.69 RPM
SRP007412_heart	0.00 RPM	29.29 RPM
SRP007412_kidney	0.05 RPM	54.26 RPM
SRP007412_liver	0.07 RPM	63.90 RPM
SRP007412_testis	0.00 RPM	87.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2814 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2814 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2814 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4142
Macaca mulatta	retro_mmul_1185

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016627	1 retrocopy	retro_cjac_460,
Homo sapiens	ENSG00000088247	1 retrocopy	retro_hsap_4142,
Macaca mulatta	ENSMMUG00000005597	1 retrocopy	retro_mmul_1185,
Monodelphis domestica	ENSMODG00000001952	1 retrocopy	retro_mdom_1386,
Otolemur garnettii	ENSOGAG00000008073	1 retrocopy	retro_ogar_884,
Pan troglodytes	ENSPTRG00000010364	1 retrocopy	retro_ptro_2814 ,