RetrogeneDB ID: retro_ptro_2833

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:67157041..67159902(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSE
• Ensembl ID: ENSPTRG00000018529
• Aliases: DSE, SART2
• Description: None

Sequence

>retro_ptro_2833
ATGAGGACTCACACACAGGGGTGCTCCTGTGTGTGTTTTTCATATATTTGCTTTGCATTGTGTCAGCCTACATCACCGAC
GAGAACCCAGAAGTCATGATTCCCTTCACCAATGCCAGCCACAACAGCCACCCCATGCTGTACTTCAGGGCAGAGGTGGC
GGAGCTGCAGCTCAGGGCGGCCAGCTGGCAGGAGCACATTGCAGCCCGCCTCACGGAGGCTGTGCACACGATGCTGTGCA
GCCCCTTGGAATACCTCCCTCCCTGGGATCCCAAGGATTACAGTGCCCGCTAGAATGAAATCTATGGAAACAACTTGGGT
GTCTTGGCAATGTTCTGTGTGCTGTATCCTGAGGACACTGAAGCCCAAGACATGGCCAAAGTCTACATGGAGAGGATGGC
AGTGCAGCCTATTTGGTTGGTGAAAGATGCTCCTTGGGATGAGGTCCCGCTTGCTCACTCCCTGGTTGGTTTTGCCACTG
CTTATGACTTCTTGCACAACTACCTGAGCAAGACACAACAGAAGAAGTTTCTTGAAGTGATTGCCAGTGCCTCAGGGTAT
ATGTATGAAAATTCATACAGGAGAGGACGGGGATTTCAATACCTGCATGATCATCAGCCCACCAACTGCATGGCTTTGCT
CACAGGAAGCCTAGTACTGACGAATCAAGGATATCTTCAAGAATCCTGCTTATGGACCAAACAAGTTCTGACCATCATGG
AGAAATCTCTGGTCTTGCTCAGGGAGATGATGGATGGCTCCCTCTATGAAAGAGTTGTGTATGGAAGCTACACAACTAGA
TCACTCTTCCAATACATGTTTCTCATCCAGAGGCACTTCAACATCAACCATGTTGGCCATCCGTGGCTTAAACAACACTT
TGCATTTATGTATAGAACCATCCTGCCAGGGTTTCAAAGGACTGTGGCTATTGAGGACTCAAATTACAACTGATTTTATG
GTCCAGAAAGCCAATTAGTTTTCCTTGATAAATTTATCATGCGTAACAGCAGTGGTAACTGGCTAGCTGACCAAATCAGA
AAGAACTGTGTGGTGGAAGGTCCAGGAACACTGTCCAAAGGGCAGCGCCAGTGCACTCTGCACACAGAATTTCTCTGGTA
TGATGCCAGCTTGAAATCAGTTCCTCCTCCAGACTTTGGCACCGCTACGCTGCATTATTTTGAAGACTGGGTGTCGTGAC
TTGAAGTGCACTACCTGCTGAAATCAATAAATCTTTCCTCTCTTTCAAGTCTGGAAAACTGGGGTGACATGCAATATGTG
ACATTGTCCACAGAAACAAATACAAAGATTGGATCAAAGGATGGAGAAATTTTAGGACAGGGCATGAACATTATGATCAA
AACTCATTTACTTTTGCTCCCAGTTGTGTGCCTTTCATTATTGAGGCTCTGTACAGGCCAAAGTACACCTTCTTCAACAA
TGTTTTGATGTTTTCCGCAGCTGTGTCAAAGAGCTGCTTTTCTCCCTGGAAGGGTCAAGTCACAGAACACTGTTCATCAA
AATGGTCTAAATACCAGCATGACCTGGCAGCTAGCTGTCAGGGGATAGTGGTTGCAGCAGAGGAGAAAAATGGGGTGGTT
TTCATCTGAGGAGAAGGTGTGGGAGCTTATAACCTCCAGCTCAACCTGAAGAATGTTCAGAGGAATCTGATCCTCCTACA
TCCACAGCTGCTTCTCCTTGTAGACCAAATACACCTGGGAGAGGAGAGTCCCCTGGAGACAGCAGCGAGCTTCTTCCACA
ATGTGGATGTTCCTTTTGAGGAGACTGTGGTAGATGGTGTCCATGGGGCTTTCATCAGGTAGAGAAATGGTCTCTATAAA
AAGTACTGGATGGACAATACTGGCTACGGCAAGAAAGCAACATTTGCATCAGTGACATATCCTGGGAGCTATCCCTACAA
TGGGACAAACTATGTGAATGTCACCATGCACCTCTGAAGTCCCATCACCAGGCCAGCTTACCTCTTCATAGGGTCACTAT
AGATGTTCAGAGCTTCACCATCCACGGAGACTCTCAGCAACTGGATGTGTTCATAGCCACCAGCGAACATGCCTACGCAA
TGTACCTGTGGACAGGTGAGGCCGCAGGACAGTCTGCCTTTGCACAGGTCATTGCTGATCATCACAAAATTCTGTTTGAC
CGGAATTCAGCCATCAAGAGCAGCATTGTCCCTGAGGTGAAGGACTATGCTGCTCTTGTGGAACAGAACCTGCAGCATTT
TAAGCCAGTGTTTCAGCTGGAGAAGCAGACACTCTCCTGAGTCCAGAACCAGCTAGCTTTAGGAAGACTGCTGACCGGCT
GCTGAGATTTTCAGATAAGAGACAGGCTGAAGAGGCCATCGACAGGATTTTTGCCATAACACAGCAACAGCAGCAGCAAA
GCAAGTCAAAGAAAAACCGAAGGGCAGGCGAATGCTATAAATTTGTGGATGCTGTCCCTGATATTTTTGCACAGATTGAG
GTCAATGAGAAAAAGATTAGACAGAAAGCTCAGATTCAGGCACAGAAAGAACTACCCATAAATGAAGATGAAGAAATGAA
AAACCTCTTAGATTTTGCAGATATAACATATGAGAAACATAAAAATGGGGCTTGATGAAAGGCCGGGTTGGACAGGCATG
GATGGTGACAACTACTCGTAGCAGGGCCTCATCACTATCTGCTTCCTATACCAGATTGTTCCTCATCCTGAACATTGCTA
TTTTCTTTGTCATGTTGGCAATACAACTGACTTTTTCCAGACGGCCCACAACCTACATGGCCAAAGATGTCTTTATGCAG
TTCTTCTAACAGATAGCTGTATTTTATTGTGGTTGTACTCTCTTGTTCTCAATCGCAGTGT

Alignment

ORF - retro_ptro_2833 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.99 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MRTHT-RGAP-SVFFIYLLCFVSAYITDENPEVMIPFTNANYDSHPMLYFSRAEVAELQRRAASSHEHIA
          MRTHT.RGAP..VFFIYLLC.VSAYITDENPEVMIPFTNA...SHPMLYF.RAEVAELQ.RAAS..EHIA
Retrocopy MRTHT>RGAP>CVFFIYLLCIVSAYITDENPEVMIPFTNASHNSHPMLYF-RAEVAELQLRAASWQEHIA

Parental  ARLTEAVHTMLSSPLEYLPPWDPKDYSARWNEIFGNNLGALAMFCVLYPENIEARDMAKDYMERMAAQPS
          ARLTEAVHTML.SPLEYLPPWDPKDYSAR.NEI.GNNLG.LAMFCVLYPE..EA.DMAK.YMERMA.QP.
Retrocopy ARLTEAVHTMLCSPLEYLPPWDPKDYSAR*NEIYGNNLGVLAMFCVLYPEDTEAQDMAKVYMERMAVQPI

Parental  WLVKDAPWDEVPLAHSLVGFATAYDFLYNYLSKTQQEKFLEVIANASGYMYETSYRRGWGFQYLHNHQPT
          WLVKDAPWDEVPLAHSLVGFATAYDFL.NYLSKTQQ.KFLEVIA.ASGYMYE.SYRRG.GFQYLH.HQPT
Retrocopy WLVKDAPWDEVPLAHSLVGFATAYDFLHNYLSKTQQKKFLEVIASASGYMYENSYRRGRGFQYLHDHQPT

Parental  NCMALLTGSLVLMNQGYLQEAYLWTKQVLTIMEKSLVLLREVTDGSLYEGVAYGSYTTRSLFQYMFLVQR
          NCMALLTGSLVL.NQGYLQE..LWTKQVLTIMEKSLVLLRE..DGSLYE.V.YGSYTTRSLFQYMFL.QR
Retrocopy NCMALLTGSLVLTNQGYLQESCLWTKQVLTIMEKSLVLLREMMDGSLYERVVYGSYTTRSLFQYMFLIQR

Parental  HFNINHFGHPWLKQHFAFMYRTILPGFQRTVAIADSNYNWFYGPESQLVFLDKFVMRNGSANWLADQIRR
          HFNINH.GHPWLKQHFAFMYRTILPGFQRTVAI.DSNYN.FYGPESQLVFLDKF.MRN.S.NWLADQIR.
Retrocopy HFNINHVGHPWLKQHFAFMYRTILPGFQRTVAIEDSNYN*FYGPESQLVFLDKFIMRNSSGNWLADQIRK

Parental  NRVVEGPGTPSKGQRWCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW-GVVTYGSALPAEINRSFLSF
          N.VVEGPGT.SKGQR.CTLHTEFLWYDASLKSVPPPDFGT.TLHYFEDW.GVVT..SALPAEIN.SFLSF
Retrocopy NCVVEGPGTLSKGQRQCTLHTEFLWYDASLKSVPPPDFGTATLHYFEDW<GVVT-*SALPAEINKSFLSF

Parental  KSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFS
          KSGKLG..AI.DIVHRNKYKDWIKGWRNF..GHEH.DQNSFTFAP..VPFI.EALY.PKYTFFNNVLMFS
Retrocopy KSGKLG*HAICDIVHRNKYKDWIKGWRNFRTGHEHYDQNSFTFAPSCVPFIIEALYRPKYTFFNNVLMFS

Parental  PAVSKSCFSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRN
          .AVSKSCFSPW.GQVTE.CSSKWSKY.HDLAASCQG.VVAAEEKNGVVFI.GEGVGAYN.QLNLKNVQRN
Retrocopy AAVSKSCFSPWKGQVTEHCSSKWSKYQHDLAASCQGIVVAAEEKNGVVFI*GEGVGAYNLQLNLKNVQRN

Parental  LILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSKK
          LILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIR.R.GLYK.YWMD.TGY.KK
Retrocopy LILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIR*RNGLYKKYWMDNTGYGKK

Parental  ATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGP-SIDVQSFTVHGDSQQLDVFIATSKHAYAT
          ATFASVTYP..YPYNGTNYVNVTMHL.SPITR.AYLFIG...IDVQSFT.HGDSQQLDVFIATS.HAYA.
Retrocopy ATFASVTYPGSYPYNGTNYVNVTMHL*SPITRPAYLFIGS<TIDVQSFTIHGDSQQLDVFIATSEHAYAM

Parental  YLWTGEATGQSAFAQVIADHHKILFDRNSVIKSSIVPEVKDYAAIVEQNLQHFKPVFQLLEKQILSRVRN
          YLWTGEA.GQSAFAQVIADHHKILFDRNS.IKSSIVPEVKDYAA.VEQNLQHFKPVFQ.LEKQ.LS.V.N
Retrocopy YLWTGEAAGQSAFAQVIADHHKILFDRNSAIKSSIVPEVKDYAALVEQNLQHFKPVFQ-LEKQTLS*VQN

Parental  -TASFRKTAERLLRFSDKRQTEEAIDRIFAISQQQQQQSKSKKNRRAGKRYKFVDAVPDIFAQIEVNEKK
          ..ASFRKTA.RLLRFSDKRQ.EEAIDRIFAI.QQQQQQSKSKKNRRAG..YKFVDAVPDIFAQIEVNEKK
Retrocopy <PASFRKTADRLLRFSDKRQAEEAIDRIFAITQQQQQQSKSKKNRRAGECYKFVDAVPDIFAQIEVNEKK

Parental  IRQKAQILAQKELPIDEDEEMKDLLDFADVTYEKHKNG-GLIKGRFGQARMVTATHSRAPSLSASYTRLF
          IRQKAQI.AQKELPI.EDEEMK.LLDFAD.TYEKHKNG.GL.KGR.GQA.MVT.T.SRA.SLSASYTRLF
Retrocopy IRQKAQIQAQKELPINEDEEMKNLLDFADITYEKHKNG<GLMKGRVGQAWMVTTTRSRASSLSASYTRLF

Parental  LILNIAIFFVMLAMQLT-YFQRSQSLHGQRCLYAVLLIDSCILLWLYS-SCSQSQC
          LILNIAIFFVMLA.QLT..FQ....LHGQRCLYAVLL.DSCILLWLYS.SCSQSQC
Retrocopy LILNIAIFFVMLAIQLT<FFQTAHNLHGQRCLYAVLLTDSCILLWLYS<SCSQSQC

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	3.52 RPM
SRP007412_cerebellum	0.00 RPM	4.66 RPM
SRP007412_heart	0.00 RPM	5.57 RPM
SRP007412_kidney	0.13 RPM	8.55 RPM
SRP007412_liver	0.00 RPM	9.75 RPM
SRP007412_testis	0.00 RPM	24.03 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2833 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2833 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2833 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4178
Gorilla gorilla	retro_ggor_2802
Pongo abelii	retro_pabe_3418

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013791	1 retrocopy	retro_acar_15,
Callithrix jacchus	ENSCJAG00000004530	1 retrocopy	retro_cjac_1174,
Homo sapiens	ENSG00000111817	1 retrocopy	retro_hsap_4178,
Gorilla gorilla	ENSGGOG00000026746	2 retrocopies	retro_ggor_1419, retro_ggor_2802,
Nomascus leucogenys	ENSNLEG00000013106	1 retrocopy	retro_nleu_2476,
Pongo abelii	ENSPPYG00000016948	2 retrocopies	retro_pabe_3418, retro_pabe_3517,
Pan troglodytes	ENSPTRG00000018529	1 retrocopy	retro_ptro_2833 ,
Sorex araneus	ENSSARG00000010799	1 retrocopy	retro_sara_560,
Takifugu rubripes	ENSTRUG00000006239	1 retrocopy	retro_trub_32,
Xenopus tropicalis	ENSXETG00000032776	1 retrocopy	retro_xtro_8,