RetrogeneDB ID: retro_ptro_2526

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:53884795..53885876(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC19A3
• Ensembl ID: ENSPTRG00000028998
• Aliases: None
• Description: solute carrier family 19, member 3 [Source:HGNC Symbol;Acc:16266]

Sequence

>retro_ptro_2526
AGCATGGTCAGCCCTGAGACACTGTCAGGAAGTGAGAGGCCACCGTAGGAGTGTCACGCTAACAGCCAACCCAGCGGCCC
CCATGAAGGCTGACGCTTGGCATCCCTGGAGAATGGGTCACGCTTTTACCTCATCGCATAGCCATAGTCTCTGCCTCCAC
AGCCTTCATTTTCTCACTTTTTCTATCAATGCCCAAGAAAAGAATGTTTTTCCATGCAAAACCCAGCAAAGAAATAAAGA
AGTCCCCAAGCCTGTGTGCAGGGTTAAAGGAACCTCATGAGAGTGAAGCACTAGGCTGTGAAGGGGAGAAACCCACTTGG
GAAAAGCCTACCACTTCGGGGAACCTGGATGACGGCCCACAAAGCATAGTGCCACAAACAGTGACTCTGAAAGTTCGTGT
TCCGTGGTTCCAAGATTTGAAGCAGTGTTACTCCTCAGAGGCCTTTGTTACTAATCCCCACAGTGGGCTTTTTCCACCAC
AGGTTTTAACCTAGCTTTGAACTATGTTCAAGTCCTATGAGGTTGCAAAGCACCACCCCAATATTCTTATACCTATAATG
GGGCACAGAAGCTACTGAAGCATTTGGTAGGGCTGTGGCTGCCTGTGCAGTGGGCTATGTGAAAATCAACTGGAGTCTCC
TGGAGAGTGGGCTCTGGAAGTCTCCTCAGTCATCGGCACAGGCTCTTGACCTCTCGTGCACTATATGACCAAAGTCTACG
CAGGCTATGTGGGCTATTTGCGATTCAAGTCCAACTATGTGCTGCTTCTAACCTAGGCAGTATTCCAGACTGCAGTCCAG
CTGAGCGTGGAATGTGTATCCTGGTGCCCGGATTCCACACCTCACTGCCTTGGTGATTCAGCAGACCCTCATCACTGTGA
CTGCAATTCATCAGAGAGGGCTTAGCCTGTGATCAGCATTCAGTTTGTAGTTTACAGGAGTTATTTTGCAGTCACTTCTA
GAATTTTCCTAATAAGAAGAATATCTAATGCCTATCAGCCAAATGCCAAGAGGAAGGAGTTCAGAGCCCTGCTATGAGTC
AGAACCCAGATGGGCCGCACCCAAAGGAGCTGAGCAGTATC

Alignment

ORF - retro_ptro_2526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.15 %
• Parental protein coverage: 72.98 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  SVVSPE-HYQRVSGYCRSVTLAAYTAGSVLAQL-LVSLANMSYFYL-NVISLASVSVAFLFSLFLPMPKK
          S.VSPE.H.Q.V.G..RSVTL.A..A....A...L.SL.N.S.FYL...I...S.S.AF.FSLFL.MPKK
Retrocopy SMVSPE>HCQEVRGHRRSVTLTANPAAPMKADA<LASLENGSRFYL<HRIAIVSASTAFIFSLFLSMPKK

Parental  SMFFQAKPSREIKKSSSVNPVLEETHEGEAPGCEEQKPTSEILSTSGKLNKGQLNSLKSSNVTVDVFVQW
          .MFF.AKPS.EIKKS.S....L.E.HE.EA.GCE..KPT.E...TSG.L..G...S.....VT..V.V.W
Retrocopy RMFFHAKPSKEIKKSPSLCAGLKEPHESEALGCEGEKPTWEKPTTSGNLDDGP-QSIVPQTVTLKVRVPW

Parental  FQDLKECYSSKR-LFYWSLWWAFATAGFNQVLNYVQILWDYKAPSQDSSIYNGA-VEAIATFGGAVAAFA
          FQDLK.CYSS...L.Y.S..WAF.T.GFN..LNYVQ.L...KAP.Q.S..YNGA..EA...FG.AVAA.A
Retrocopy FQDLKQCYSSEA<LCY*SPQWAFSTTGFNLALNYVQVL*GCKAPPQYSYTYNGA<TEATEAFGRAVAACA

Parental  VGYVKVNWDLL-GELALAVFSVVNAGSLFLMHYTANIWACYAGYLIFKSSYMLLITIAVFQIAVNLNVER
          VGYVK.NW.LL.GE.AL.V.SV...GS..L.HY.....A.Y.GYL.FKS.Y.LL.T.AVFQ.AV.L.VE.
Retrocopy VGYVKINWSLL<GEWALEVSSVIGTGS*PLVHYMTKVYAGYVGYLRFKSNYVLLLT*AVFQTAVQLSVEC

Parental  YA-LVFGINTFI-ALVI-QTIMTVIVVDQRGLNL-PVSIQFLVYGSYFAVIAGIFLMRSMYIIY-STKSQ
          ...LV.G..T...ALVI.QT..TV....QRGL.L...SIQF.VY.SYFAV...IFL.R.....Y.S.K.Q
Retrocopy VS<LVPGFHTSL<ALVIQQTLITVTAIHQRGLSL<VISIQFVVYRSYFAVTSRIFLIRRISNAY<SAKCQ

Parental  KD-VQSPAPSENPGVSHPEEESNI
          ...VQSPA.S.NP...HP.E.S.I
Retrocopy EEGVQSPAMSQNPDGPHPKELSSI

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	2.59 RPM
SRP007412_cerebellum	0.36 RPM	1.72 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	2.54 RPM
SRP007412_liver	0.00 RPM	4.55 RPM
SRP007412_testis	0.00 RPM	0.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2526 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2526 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2526 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3732

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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 ,