RetrogeneDB ID: retro_ggor_2518

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:56442831..56443740(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC19A3
• Ensembl ID: ENSGGOG00000004344
• Aliases: None
• Description: None

Sequence

>retro_ggor_2518
AGCATGGTCAGCCCTGAGACACTGTCAGGAAGTGAGAGGCCACCGTAGGAGTGTCACTCTAACAGCCAACCCAGCTGCCC
CCATGAAGGCTGACGCTTGGCATCCCTGGAGAATGGGTCACACTTTCACCTCATCGCATAGCCATAGTCTCTGCCTCCAC
AGCCTTCATTTTCTCACTTTTTCTATCAATGCCCAAGAAAAGAATGTTTTTCCATGCAAAACCCAGCAAAGAAATAAAGA
AGTCCCCAAGCCTGTGTGCAGGGTTAAAGGAACCTCATGAGAGTGAAGCACTAGGCTGTGAAGGGGAGAAACCCACTTGG
GAAAAGCCCACCACTTCGGGGAACCTGGATGACGGCCCATAGAGCATAGTGCCACAAACAGTGACTCTGAAAGTTCGTGT
TCCATGGTTCCAAGATTTGAAGTAGTGTTACTCCTCAGAGGCCTTTGTTACTAATCCCCATGGTGGGCTTTTTCCACCAC
AGGTTTTAACCTAGCTTTGAACTATGTTCAAGTCCTATGAGGTTGCAAAGCACCACCCCAATATTCTTATACCTATAATG
GGGCACAGAAGCTACTGAAGCATTTGGTAGGGCTGTGGCTGCCTGTGCAGTGGGCTATGTGAAAATCAACTGGAGTCTCC
TGGAGAGTGGGCTCTGGAAGTCTCCTCAGTCATCAACGCAGGCTCTTGACCTCTCGTGCACTACATGACCAAAGTCTACG
CAGGCTATGTGGGCTATTTGCAATTCAAGTCCAGCTATGTGCTGCTTCTAACCCAGGCAGTATTCCAGACTGCAGTCCAG
CTAAGCGTGGAATGTGTATCCTGGTGCCCGGATTCCACACCTCACTGCCTTGGTGATTCAGCAGACCCTCATCACTGTGA
CTGCAATTCATCAGAAAGGGCTCAGCCTG

Alignment

ORF - retro_ggor_2518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.64 %
• Parental protein coverage: 69.63 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

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

Parental  SMFFHAKPSREIKKSSSVNPVLEETHEGEAPGCEEQKPTSEILSTSGKLNKGQLNSLKPSNVTVDVFVQW
          .MFFHAKPS.EIKKS.S....L.E.HE.EA.GCE..KPT.E...TSG.L..G...S..P..VT..V.V.W
Retrocopy RMFFHAKPSKEIKKSPSLCAGLKEPHESEALGCEGEKPTWEKPTTSGNLDDGP-*SIVPQTVTLKVRVPW

Parental  FQDLKECYSS-KRLFYWSLWWAFATAGFNQVLNYVQILWDYKAPSQDSSIYNGA-VEAIATFGGAVAAFA
          FQDLK.CYSS...L.Y.S.WWAF.T.GFN..LNYVQ.L...KAP.Q.S..YNGA..EA...FG.AVAA.A
Retrocopy FQDLK*CYSS<RGLCY*SPWWAFSTTGFNLALNYVQVL*GCKAPPQYSYTYNGA<TEATEAFGRAVAACA

Parental  VGYVKVNWDLL-GELALAVFSVVNAGSLFLMHYTANIWVCYAGYLIFKSSYMLLITIAVFQIAVNLNVER
          VGYVK.NW.LL.GE.AL.V.SV.NAGS..L.HY.......Y.GYL.FKSSY.LL.T.AVFQ.AV.L.VE.
Retrocopy VGYVKINWSLL<GEWALEVSSVINAGS*PLVHYMTKVYAGYVGYLQFKSSYVLLLTQAVFQTAVQLSVEC

Parental  YA-LVFGINTFI-ALVI-QTIMTVIVVDQRGLNL
          ...LV.G..T...ALVI.QT..TV....Q.GL.L
Retrocopy VS<LVPGFHTSL<ALVIQQTLITVTAIHQKGLSL

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	1.10 RPM
SRP007412_cerebellum	0.00 RPM	0.87 RPM
SRP007412_heart	0.00 RPM	0.13 RPM
SRP007412_kidney	0.04 RPM	4.42 RPM
SRP007412_liver	0.00 RPM	2.59 RPM
SRP007412_testis	0.00 RPM	1.45 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2518 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2518 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3209

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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,