RetrogeneDB ID: retro_pabe_3517

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9_random:9243815..9246041(+)
• 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_3517
CTCACAAGAAGCCTAGTCCTGACGAATCAAGGATATCTTCAAGAAGCTGCTTGTGGACCAAACAAGTTCTGACCATCATG
GAGAAATCTCTGGTCTTGCTCAGGGAGATGATGGATGGCTCCCTCTATCAAAGAGTTGTTATGGAAGCTACACCACTAGA
TCACTCTTCCAATACATGTTTCTCATCCAGAGGCACTTCAACATCAACCACGTTGGCCATCCATGGCTTAAACAACACTT
TGCATTTATGTATTGAACCATCCTGCCAGGGTTTCAAAGGACTGTGGCTATTGCAGACTCAAATTACAACTGATTTTGTG
GTCCAGAAAGCCAATTAGTGTTCCTTGATAAATTTGTCATGCGTAACAGCAATGGTAACTGGCTAGCTGACCAAATCAGA
AGGAACCGTGTGGTGGAAGGTCCAGGAACACTGTCCAAAGGGCAGCGCTTGTGCACTCTGCACACAGAATTTCTCTGGTA
TGATGCCAGCTTGAAATCCGTTCCTCCTCCAGACTTTGGCACCCCTACACTGCATTATTTTGAAGACTGGGTGTCGTGAC
TTATGGAAGTGCACTACCTGCTGAAATCAATAAATCTTTCCTCTCTTTCAAGTCTGGAAAACTGGGGGGACATGCAATAT
GTGACATTGTCCACAGAAACAAATACAAAGATTAGATCAAAGGATGGAGAAATTTTAGGGCAGGGCATGAACATTATGAT
CAAAACTCATTTACTTTTGCTCTCAGTTGTGTGCCTTTCATTATTGAGGCTCTGTATGGGCCAAAGTACACCTTCTTCAA
CAATGTTTTGATGTTTTCTGCAGTTGTGTCAAAGAGCTGCTTTTCTCCCTGGAATGGTCAAGTCACAGAAGACTGTTCAT
CAAAATGGTCTAAATACCAGCATGACCTGGCAGCTAGCTGTCAAGGGACAGTGGTTGCAGCAGAGGAGAAAAATGGGGTG
GTTTTCATCTGAGGAGAAGGTGTGGGAGCTTATAACCCCCAGCTCAACCTGAAGAATGTTCAGAGGAATCTGATCCTCCT
ACGTCCACAGCTGCTTCTCCTTGTAGACCAAATACACCTGGGAGAGGAGAGTCCCTTGGAGATAGCAGCGAGCTTCTTCC
ACAATGTGGATGTTCCTTTTGAGGAGACTGTGGTAGATGGCATCCATGGGGCTTTCTTCAGGTAGTGAGATGGTCTCTAT
AAAAAGTACTGGATGGACAATACTGGCTACAGCAAGAAAGCAACATTTGCCTCAGTGACATATCCTGGGAGCTATCCCTA
CAATGGGACAAACTATGTGAATGTCACCATGCACCTCTGAAGTCCCATCACCAGGCCAGCTTACCTCTTCATACGGTCAT
CTATAGATGTTCAGAGCTTCACCATCCACAGAGACTCTCAGCAACTGGATGTGTTCATAGCCACCAGTGAACATGCCTAC
GTAACATACCTGTGGACAGGTGAGGCCACAGGACAGTCTGCTTTTGCACAGGTCATTGCTGATCATCACAAAATTCTGTT
TGACTGGAATTCAGCCATCAAGAGCAGCATTGTCCCTGAGGTGAAGAACTATGCTGCTATTGTGGAACAGAACCTGCAGC
ATTTTAAGCCAGTGTTTCAGCTGGAGAAGCAGATACTGTCCTGAGTCCAGAACCAGCTAGCTTTAGGAAGACTGCTGACC
ACCTGCTGAGATTTTCAGATAAGAGACAGGCTGAAGAGGCCATCGACAGGATTTTTGCCATAACACAGCAACAGCAGCAG
CAAAGCAAGTCAAAGAAAAACCAAAGGGCAGGTGAACGCTATAAATTTGTGGACGCTGTCCCTGATATTTTTACACAGAT
TGAGGTCAATGAGAAAAAGATTAGACAGAAAGCTCAGATTCAGGCACAGAAAGAACTACCCATAAATGAAGATGAAGAAA
TGAAAAACCTCTTAGATTTTGCAGATGTAACATATGAAAACATAAAAATGGGGCTTGATGAAAGGCCGGGTTGGACAGGC
ATGGATGGTGACAACCACTCGTAGCAGGGCCTCATCACTATCTGCTTCCTACACCAGATTGTTCCTCATCCTGAACATTG
CTATCTTCTTTGTCATGTTGGCAATACAACTGACTTATTTCCAGAGGGCCCAGAACCTACATGGCCAAAGACGTCTTTAT
GCAGTTCTTCTAATAGATAGCTGTATTTTATTGTGGTTGTACTCTTCTTGTTCCCAATCACAATGT

Alignment

ORF - retro_pabe_3517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.55 %
• Parental protein coverage: 77.77 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LTGSLVLMNQGYLQEAY-LWTKQVLTIMEKSLVLLREVTDGSLYEGVA-YGSYTTRSLFQYMFLVQRHFN
          LT.SLVL.NQGYLQEA..LWTKQVLTIMEKSLVLLRE..DGSLY..V..YGSYTTRSLFQYMFL.QRHFN
Retrocopy LTRSLVLTNQGYLQEAA<LWTKQVLTIMEKSLVLLREMMDGSLYQRVV<YGSYTTRSLFQYMFLIQRHFN

Parental  INHFGHPWLKQHFAFMYRTILPGFQRTVAIADSNYNWFYGPESQLVFLDKFVMRNGSGNWLADQIRRNRV
          INH.GHPWLKQHFAFMY.TILPGFQRTVAIADSNYN.F.GPESQLVFLDKFVMRN..GNWLADQIRRNRV
Retrocopy INHVGHPWLKQHFAFMY*TILPGFQRTVAIADSNYN*FCGPESQLVFLDKFVMRNSNGNWLADQIRRNRV

Parental  VEGPGTPSKGQRWCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW-GVVTYGSALPAEINRSFLSFKSG
          VEGPGT.SKGQR.CTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW.GVVTYGSALPAEIN.SFLSFKSG
Retrocopy VEGPGTLSKGQRLCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW<GVVTYGSALPAEINKSFLSFKSG

Parental  KLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAV
          KLGG.AI.DIVHRNKYKD.IKGWRNF.AGHEH.DQNSFTFA...VPFI.EALYGPKYTFFNNVLMFS..V
Retrocopy KLGGHAICDIVHRNKYKD*IKGWRNFRAGHEHYDQNSFTFALSCVPFIIEALYGPKYTFFNNVLMFSAVV

Parental  SKSCFSPWEGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLIL
          SKSCFSPW.GQVTEDCSSKWSKY.HDLAASCQG.VVAAEEKNGVVFI.GEGVGAYNPQLNLKNVQRNLIL
Retrocopy SKSCFSPWNGQVTEDCSSKWSKYQHDLAASCQGTVVAAEEKNGVVFI*GEGVGAYNPQLNLKNVQRNLIL

Parental  LHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKATF
          L.PQLLLLVDQIHLGEESPLE.AASFFHNVDVPFEETVVDG.HGAF.R..DGLYK.YWMD.TGYS.KATF
Retrocopy LRPQLLLLVDQIHLGEESPLEIAASFFHNVDVPFEETVVDGIHGAFFR**DGLYKKYWMDNTGYSKKATF

Parental  ASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSIDVQSFTVHGDSQQLDVFVATSKHAYATYLWT
          ASVTYP..YPYNGTNYVNVTMHL.SPITR.AYLFI..SIDVQSFT.H.DSQQLDVF.ATS.HAY.TYLWT
Retrocopy ASVTYPGSYPYNGTNYVNVTMHL*SPITRPAYLFIRSSIDVQSFTIHRDSQQLDVFIATSEHAYVTYLWT

Parental  GEATGQSAFAQVIADRHKILFDRNSAIKSSIVPEVKDYAAIVEQNLQHFKPVFQLLEKQILSRVRN-TAS
          GEATGQSAFAQVIAD.HKILFD.NSAIKSSIVPEVK.YAAIVEQNLQHFKPVFQ.LEKQILS.V.N..AS
Retrocopy GEATGQSAFAQVIADHHKILFDWNSAIKSSIVPEVKNYAAIVEQNLQHFKPVFQ-LEKQILS*VQN<PAS

Parental  FRKTAERLLRFSDKRQTEEAIDRIFAISQQQQQQSKSKKNRRAGKRYKFVDAVPDIFAQIEVNEKKIRQK
          FRKTA..LLRFSDKRQ.EEAIDRIFAI.QQQQQQSKSKKN.RAG.RYKFVDAVPDIF.QIEVNEKKIRQK
Retrocopy FRKTADHLLRFSDKRQAEEAIDRIFAITQQQQQQSKSKKNQRAGERYKFVDAVPDIFTQIEVNEKKIRQK

Parental  AQILAQKELPIDEDEEMKDLLDFADVTYE-KHKNG-GLIEGRFGQARMVTTTHSRAPSLSASYTRLFLIL
          AQI.AQKELPI.EDEEMK.LLDFADVTYE.KHKNG.GL..GR.GQA.MVTTT.SRA.SLSASYTRLFLIL
Retrocopy AQIQAQKELPINEDEEMKNLLDFADVTYE<KHKNG<GLMKGRVGQAWMVTTTRSRASSLSASYTRLFLIL

Parental  NIAIFFVMLAMQLTYFQKAQSLHGQRCLYAVLLIDSCILLWLYSSCSQSQC
          NIAIFFVMLA.QLTYFQ.AQ.LHGQR.LYAVLLIDSCILLWLYSSCSQSQC
Retrocopy NIAIFFVMLAIQLTYFQRAQNLHGQRRLYAVLLIDSCILLWLYSSCSQSQC

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_3517 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3517 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3517 has 0 orthologous retrocopies within eutheria group .

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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,