RetrogeneDB ID: retro_pabe_3209

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7_random:14876490..14877751(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC19A3
• Ensembl ID: ENSPPYG00000013242
• Aliases: None
• Description: solute carrier family 19, member 3 [Source:HGNC Symbol;Acc:16266]

Sequence

>retro_pabe_3209
CTGCTCCCAGTGTCTGTCTTCTCGAGTCACCACAAGCCCATCACCCTCTCATAAGGGCTCTGCTTCATCATTCCCCAGCT
GCTGCTCTTGTTGGGCTAAGGGATGAAGACTACACTGGCTGTCAAGTTCTCCTCCAGGATACTCACCACCTCCCAGGTGG
CCTACTGTATCAACCCATGCAGCATGGTCAGCCCTGAGACACTGTCAGGAAGTGAGAGGCCACTGTAGGAGTGTCACGCT
AACAGCCAACCCAGCGGCCCCCATGAAGGCTGATGCTTGGCATCCCTGGAGAATGGGTCACACTTTTACCTCATTGCATA
GCCATAGTCTCTGCCTCCACAGCCTTCATTTTCTCACTTTTTCTATCAATGCCCAAGAAAAGCATGTTTTTCCATGCAAA
ACCCAGCAAAGAAATAAAGAAGTCCCCAAGCCTGTGTGCAGGGTTAAAGGAACCTCATGAGAGTGAAGCATTAGGCTGTG
AAGGGGAGAAACCCACTTGGGAAAAGCCCACCACTTCGGGGAACCTGGATGACGGCCCACAGAGCATAGTGCCACAAACA
GTGACTCTGAAAGCTCGTGTTCCGTGGTTCCAAGATTTGAAGTAGTGTTACTCCTCAGAGGCCTTTGTTACTAATCTCCA
TGGTGGGCTTTTTCCACCACAGGTTTTAACCTAGCTTTGAACTATGTTCAAGTCCTATGAGGTTGCAAAGCACCACCCCA
ATATTCTTATACCTATAATGGGGCACAGAAGCTACTGAAGCATTTGGTAGGGCTGTGGCTGCCTGTGCAGTGGGCTATGT
GAAAATCAACTGGAGTCTCCTGGAGAGTGGGCTCTGGAAGTCTCCTCAGTCATCAGCGCAGGCTCTTGACCTCTCCTGCA
CTACATGACCAAAGTCTACGCAGGCTATGTGGGCTATTTGCGATTCAAGTCCAACTATGTGCTGCTTCTAACCCAGGCAG
TATTCCAGACTGCAGTCAAGCTGAGCGTGGAATGTGTATCCTGGTGTCCGGATTCCATACCTCACTGCCTTGGTGATTCA
GCAGACCTTCATCACTGTGACTGCAATTCATCAGAGAGGGCTCAGCCTGTGATCAGCATTCAGTTTGTAGTTTACAGGAG
TTATTTTGCAGTCACTTCTAGAATTTTCCTAATAAGAAGAATATCTAATGCCTATCAGCCAAATGCCAAGAGGAAGGAGT
TCAGAGCCCTGCTATGAGTCAGAACCCAGATGGGCCGCACCCAAAGGAGCTGAGCAGTATC

Alignment

ORF - retro_pabe_3209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.05 %
• Parental protein coverage: 82.33 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  LLPVFVLTDYVRYKPVIILQGISFIITWLLLLFGQGVKTMQVVEFFYGMVTAAEVAYYAYIYSVVSPE-H
          LLPV.V.......KP.....G..FII..LLLL.G.G.KT...V.F.....T...VAY.....S.VSPE.H
Retrocopy LLPVSVFSSH--HKPITLS*GLCFIIPQLLLLLG*GMKTTLAVKFSSRILTTSQVAYCINPCSMVSPE>H

Parental  YQRVSGYCRSVTLAAYTAGSVLAQL-LVSLANLSYFYL-HVISLASVSVAFLFSLFLPMPKKSMFFHAKP
          .Q.V.G.CRSVTL.A..A....A...L.SL.N.S.FYL.H.I...S.S.AF.FSLFL.MPKKSMFFHAKP
Retrocopy CQEVRGHCRSVTLTANPAAPMKADA<LASLENGSHFYL<HCIAIVSASTAFIFSLFLSMPKKSMFFHAKP

Parental  SREIKKSSSVKPVLEETHGGEAPGCEEQKPTSEILSTSGKPNKGQLNSLKPSSVTVEVFVQWFQDLKECY
          S.EIKKS.S....L.E.H..EA.GCE..KPT.E...TSG....G...S..P..VT....V.WFQDLK.CY
Retrocopy SKEIKKSPSLCAGLKEPHESEALGCEGEKPTWEKPTTSGNLDDGP-QSIVPQTVTLKARVPWFQDLK*CY

Parental  SS-KRLFYWSLWWAFATAGFNQVLNYVQILWDYKAPSQDSSIYNGA-VEAIATFGGAVAAFAVGYVKVNW
          SS...L.Y.S.WWAF.T.GFN..LNYVQ.L...KAP.Q.S..YNGA..EA...FG.AVAA.AVGYVK.NW
Retrocopy SS<RGLCY*SPWWAFSTTGFNLALNYVQVL*GCKAPPQYSYTYNGA<TEATEAFGRAVAACAVGYVKINW

Parental  DLL-GELALAVFSVVNAGSLFLMHYTANIWACYAGYLIFKSSYMLLITIAVFQIAVNLNVERYA-LVFGI
          .LL.GE.AL.V.SV..AGS..L.HY.....A.Y.GYL.FKS.Y.LL.T.AVFQ.AV.L.VE....LV.G.
Retrocopy SLL<GEWALEVSSVISAGS*PLLHYMTKVYAGYVGYLRFKSNYVLLLTQAVFQTAVKLSVECVS<LVSGF

Parental  NTFI-ALVI-QTIMTVIVVDQRGLNL-PVSIQFLVYGSYFAVIAGIFLMRSMYIIY-STKSQKD-VQSPA
          .T...ALVI.QT..TV....QRGL.L...SIQF.VY.SYFAV...IFL.R.....Y.S.K.Q...VQSPA
Retrocopy HTSL<ALVIQQTFITVTAIHQRGLSL<VISIQFVVYRSYFAVTSRIFLIRRISNAY<SAKCQEEGVQSPA

Parental  PSENPDVSHPEEESNI
          .S.NPD..HP.E.S.I
Retrocopy MSQNPDGPHPKELSSI

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	0.06 RPM	0.94 RPM
SRP007412_cerebellum	0.12 RPM	2.07 RPM
SRP007412_heart	0.00 RPM	0.36 RPM
SRP007412_kidney	0.07 RPM	0.76 RPM
SRP007412_liver	0.00 RPM	6.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3209 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3209 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3209 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2518

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000135917	1 retrocopy	retro_hsap_3732,
Gorilla gorilla	ENSGGOG00000004344	1 retrocopy	retro_ggor_2518,
Monodelphis domestica	ENSMODG00000021220	1 retrocopy	retro_mdom_955,
Mustela putorius furo	ENSMPUG00000001374	1 retrocopy	retro_mputfur_1211,
Nomascus leucogenys	ENSNLEG00000013501	1 retrocopy	retro_nleu_2561,
Pongo abelii	ENSPPYG00000013242	1 retrocopy	retro_pabe_3209 ,
Pan troglodytes	ENSPTRG00000028998	1 retrocopy	retro_ptro_2526,