RetrogeneDB ID: retro_pabe_3418

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:63285822..63288687(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSE
• Ensembl ID: ENSPPYG00000016948
• Aliases: None
• Description: dermatan sulfate epimerase [Source:HGNC Symbol;Acc:21144]

Sequence

>retro_pabe_3418
ATGAGGACTCACACACAGGGGTGCTCCCAGTGTGTTTTTCGTATATTTGCTTTGCATTGTGTCAGCCTACATCACCGACG
AGAACCCAGAAGTCATGATTCCCTTCACCAATGCCAACCACAATAGCCACCCCATGCTGTACTTCAGGGCAGAGGTGGCA
GAGCTGCAGCTCAGGGCGGCCAGCTTGCAGGAGCACATTGTAGCCCGCCTCATGGAGGCTGTGCACACGATGCTGTGCAG
CCCCTTGGAATACCTCCCTTCCTGGGATCCCAAGGATTACAGTGCCCGCTAGAATGAAATCTACGGAAACAACTTGGGTG
CCTTGGCACTGTTCTGAGTGCTGTATCCTGAGGACACTGAAGCCTGAGACATGGCCAAAGTCTACATGGACAGGATGGCA
GTGCAGCCTATCTGGTTGGTGAAAGATACTCCTTGGGATGAGGTCCCGCTTGCTCACTCCCTGTTTGGTTTTGCCACTGC
TTATGACTTCTTGTACAACTACCTGAGCAAGACACAACAGGAGAAGTTTCTTGAAGTGATTGCCAGTGCCTCAGGGTATA
TGTATGAAAATTAATACAGGAGAGGATGGGGATTTCAATACCTGCACAATCATCAGCCCACCAACTGCATGGCTTTGCTC
ACAGGAAGCCTAGTCCTGACAAATCAAGGATATCTTCAAGAAGCCTGCTTGTGGACCAAACAAGTTCTGACCATCATGGA
GAAATCTCTGGTCTTGCTCAGGGAGATGATGGATGGCTCCCTCTATGAAAGAGTTGTGTATGGAAGCTATACCACTAGAT
CACTCTTCCAATACATGTTTCTCATCCAGAGGCACTTCAACATCAACCACGTTGGTCATCCATGGCTTAAACAACACTTT
GCATTTATGTATTGAACCATCCTGCCAGGGTTTCAAAGGACTGTGGCTATTGCAGACTCAAATTACAACTGATTTTATGG
TCCAGAAAGCCAATTAGTGTTCCTTGATAAATTTGTCATGCGTAACAGCAATGGTAACTGGCTAGCTGACCAAATCAGAA
GGAACCGTGTGGTGGAAGGTCCAGGAACACTGTCCAAAGGGCAGCGCTGGTGCACTCTGCACACAGAATTTCTCTGGTAT
GATGCCAGCTTGAAATCCGTTCCTCCTCCAGACTTTGGCACCCCTACACTGCATTATTTTGAAGACTGGGTGTCGTGACT
TATGGAAGTGCACTACCTGCTGAAATCAATAAATCTTTCCTCTCTTTCAAGTCTGGAAAACTGGGGGGACATGCAATATG
TGACATTGTCCACAGAAACAAATACAAAGATTAGATCAAAGGATGGAGAAATTTTAGGGCAGGGCATGAACATTATGATC
AAAACTCATTTACTTTTGCTCTCAGTTGTGTGCCTTTCATTATTGAGGCTCTGTATGGGCCAAAGTACACCTTCTTCAAC
AATGTTTTGATGTTTTCTGCAGTTGTGTCAAAGAGCTGCTTTTCTCCCTGGAATGGTCAAGTCACAGAAGACTGTTGATC
AAAATGGTCTAAATACCAGCATGACCTGGCAGCTAGCTGTCAAGGGACAGTGGTTGCAGCAGAGGAGAAAAATGGGGTGG
TTTTCATCTGAGGAGAAGGTGTGGGAGCTTATAACCCCCAGCTCAACCTGAAGACTGTTCAGAGGAATCTGATCCTCCTA
CGTCCACAGCTGCTTCTCCTTGTAGACCAAATACACCTGGGAGAGGAGAGTCCCTTGGAGATAGCAGCGAGCTTCTTCCA
CAATGTGGATGTTCCTTTTGAGGAGACTGTGGTAGATGGCATCCATGGGGCTTTCTTCAGGTAGTGAGATGGTCTCTATA
AAAAGTACTGGATGGACAATACTGGCTACAGCAAGAAAGCAACATTTGCCTCAGTGACATATCCTGGGAGCTATCCCTAC
AATGGGACAAACTATGTGAATGTCACCATGCACCTCTGAAGTCCCATCACCAGGCCAGCTTACCTCTTCATACGGTCATC
TATAGATGTTCAGAGCTTCACCATCCACGGAGACTCTCAGCAACTGGATGTGTTCGTAGCCACCAGTGAACATGCCTACG
TAACGTACCTGTGGACAGGTGAGGCCACAGGACAGTCTGCTTTTGCACAGGTCATTGCTGGTCATCACAAAATTCTGTTT
GACTGGAATTCAGCCATCAAGAGCAGCATTGTCCCTGAGGTGAAGAACTATGCTGCTATTGTGGAACAGAACCTGCAGCA
TTTTAAGCCAGTGTTTCAGCTGGAGAAGCAGATACTGTCCTGAGTCCAGAATCAGCTAGCTTTAGGAAGACTGCTGACCA
CCTGCTGAGATTTTCAGATAAGAGACAGGCTGAAGACGCCATCGACAGGATTTTTGCCATAACACAGCAACAGCAGCAGC
AAAGCAAGTCAAAGAAAAACCAAAGGGCAGGTGAACGCTATAAATTTGTGGACGCTGTCCCTGATATTTTTACACAGATT
GAGGTCAATGAGAAAAAGATTAGACAGAAAGCTCAGATTCAGGCACAGAAAGAACTACCCATAAATGAAGATGAAGAAAT
GAAAAACCTCTTAGATTTTGCAGATGTAACATATGAAAACATAAAAATGGGGCTTGATGAAAGGCCGGGTTGGACAGGCA
TGGATGGTGACAACCACTCGTAGCAGGGCCTCATCACTATCTGCTTCCTACACCAGATTGTTCCTCATTCTGAACATTGC
TATCTTCTTTGTCATGTTGGCAATACAACTGACTTATTTCCAGAGGGCCCAGAACCTACATGGCCAAAGACGTCTTTATG
CAGTTCTTCTAATAGATAGCTGTATTTTATTGTGGTTGTACTCTTCTTGTTCCCAATCACAGTGT

Alignment

ORF - retro_pabe_3418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 13
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MRTHT-RGAPSVFFIYLLCFVSAYITDENPEVMIPFTNANYDSHPMLYFSRAEVAELQRRAASSHEHIAA
          MRTHT.RGAPSVFF.YLLC.VSAYITDENPEVMIPFTNAN..SHPMLYF.RAEVAELQ.RAAS..EHI.A
Retrocopy MRTHT>RGAPSVFFVYLLCIVSAYITDENPEVMIPFTNANHNSHPMLYF-RAEVAELQLRAASLQEHIVA

Parental  RLTEAVHTMLSSPLEYLPPWDPKDYSARWNEIYGNNLGALAMFCVLYPENIEARDMAKDYMERMAAQPSW
          RL.EAVHTML.SPLEYLP.WDPKDYSAR.NEIYGNNLGALA.F.VLYPE..EA.DMAK.YM.RMA.QP.W
Retrocopy RLMEAVHTMLCSPLEYLPSWDPKDYSAR*NEIYGNNLGALALF*VLYPEDTEA*DMAKVYMDRMAVQPIW

Parental  LVKDAPWDEVPLAHSLVGFATAYDFLYNYLSKTQQEKFLEVIANASGYMYETSYRRGWGFQYLHNHQPTN
          LVKD.PWDEVPLAHSL.GFATAYDFLYNYLSKTQQEKFLEVIA.ASGYMYE..YRRGWGFQYLHNHQPTN
Retrocopy LVKDTPWDEVPLAHSLFGFATAYDFLYNYLSKTQQEKFLEVIASASGYMYEN*YRRGWGFQYLHNHQPTN

Parental  CMALLTGSLVLMNQGYLQEAYLWTKQVLTIMEKSLVLLREVTDGSLYEGVAYGSYTTRSLFQYMFLVQRH
          CMALLTGSLVL.NQGYLQEA.LWTKQVLTIMEKSLVLLRE..DGSLYE.V.YGSYTTRSLFQYMFL.QRH
Retrocopy CMALLTGSLVLTNQGYLQEACLWTKQVLTIMEKSLVLLREMMDGSLYERVVYGSYTTRSLFQYMFLIQRH

Parental  FNINHFGHPWLKQHFAFMYRTILPGFQRTVAIADSNYNWFYGPESQLVFLDKFVMRNGSGNWLADQIRRN
          FNINH.GHPWLKQHFAFMY.TILPGFQRTVAIADSNYN.F............FVMRN..GNWLADQIRRN
Retrocopy FNINHVGHPWLKQHFAFMY*TILPGFQRTVAIADSNYN*FXXXXXXXXXXXXFVMRNSNGNWLADQIRRN

Parental  RVVEGPGTPSKGQRWCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW-GVVTYGSALPAEINRSFLSFK
          RVVEGPGT.SKGQRWCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW.GVVTYGSALPAEIN.SFLSFK
Retrocopy RVVEGPGTLSKGQRWCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW<GVVTYGSALPAEINKSFLSFK

Parental  SGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSP
          SGKLGG.AI.DIVHRNKYKD.IKGWRNF.AGHEH.DQNSFTFA...VPFI.EALYGPKYTFFNNVLMFS.
Retrocopy SGKLGGHAICDIVHRNKYKD*IKGWRNFRAGHEHYDQNSFTFALSCVPFIIEALYGPKYTFFNNVLMFSA

Parental  AVSKSCFSPWEGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNL
          .VSKSCFSPW.GQVTEDC.SKWSKY.HDLAASCQG.VVAAEEKNGVVFI.GEGVGAYNPQLNLK.VQRNL
Retrocopy VVSKSCFSPWNGQVTEDC*SKWSKYQHDLAASCQGTVVAAEEKNGVVFI*GEGVGAYNPQLNLKTVQRNL

Parental  ILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKA
          ILL.PQLLLLVDQIHLGEESPLE.AASFFHNVDVPFEETVVDG.HGAF.R..DGLYK.YWMD.TGYS.KA
Retrocopy ILLRPQLLLLVDQIHLGEESPLEIAASFFHNVDVPFEETVVDGIHGAFFR**DGLYKKYWMDNTGYSKKA

Parental  TFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSIDVQSFTVHGDSQQLDVFVATSKHAYATYL
          TFASVTYP..YPYNGTNYVNVTMHL.SPITR.AYLFI..SIDVQSFT.HGDSQQLDVFVATS.HAY.TYL
Retrocopy TFASVTYPGSYPYNGTNYVNVTMHL*SPITRPAYLFIRSSIDVQSFTIHGDSQQLDVFVATSEHAYVTYL

Parental  WTGEATGQSAFAQVIADRHKILFDRNSAIKSSIVPEVKDYAAIVEQNLQHFKPVFQLLEKQILSRVRN-T
          WTGEATGQSAFAQVIA..HKILFD.NSAIKSSIVPEVK.YAAIVEQNLQHFKPVFQ.LEKQILS.V.N..
Retrocopy WTGEATGQSAFAQVIAGHHKILFDWNSAIKSSIVPEVKNYAAIVEQNLQHFKPVFQ-LEKQILS*VQN<S

Parental  ASFRKTAERLLRFSDKRQTEEAIDRIFAISQQQQQQSKSKKNRRAGKRYKFVDAVPDIFAQIEVNEKKIR
          ASFRKTA..LLRFSDKRQ.E.AIDRIFAI.QQQQQQSKSKKN.RAG.RYKFVDAVPDIF.QIEVNEKKIR
Retrocopy ASFRKTADHLLRFSDKRQAEDAIDRIFAITQQQQQQSKSKKNQRAGERYKFVDAVPDIFTQIEVNEKKIR

Parental  QKAQILAQKELPIDEDEEMKDLLDFADVTYE-KHKNG-GLIEGRFGQARMVTTTHSRAPSLSASYTRLFL
          QKAQI.AQKELPI.EDEEMK.LLDFADVTYE.KHKNG.GL..GR.GQA.MVTTT.SRA.SLSASYTRLFL
Retrocopy QKAQIQAQKELPINEDEEMKNLLDFADVTYE<KHKNG<GLMKGRVGQAWMVTTTRSRASSLSASYTRLFL

Parental  ILNIAIFFVMLAMQLTYFQKAQSLHGQRCLYAVLLIDSCILLWLYSSCSQSQC
          ILNIAIFFVMLA.QLTYFQ.AQ.LHGQR.LYAVLLIDSCILLWLYSSCSQSQC
Retrocopy ILNIAIFFVMLAIQLTYFQRAQNLHGQRRLYAVLLIDSCILLWLYSSCSQSQC

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	4.48 RPM
SRP007412_cerebellum	0.00 RPM	3.16 RPM
SRP007412_heart	0.00 RPM	6.92 RPM
SRP007412_kidney	0.07 RPM	5.77 RPM
SRP007412_liver	0.00 RPM	15.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3418 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3418 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3418 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4178
Pan troglodytes	retro_ptro_2833
Gorilla gorilla	retro_ggor_2802

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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,