RetrogeneDB ID: retro_ptro_342

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:131964901..131965405(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SIP1
• Ensembl ID: ENSPTRG00000006291
• Aliases: SIP1, GEMIN2
• Description: None

Sequence

>retro_ptro_342
AAGTTGAAAAGGAAGCAAGGTGTGAAGGTTTCTCTTTTAGGATGCCAACCTGCCCCTGAAGGTTATTCCCCAATACTTCA
GTGGCAATAGAAAGTGGCACCGTTTTCAACGTAAGACAGAATGTGCACAAACATAGAAGTCACTGGAAATCACGACAGTT
GGATAGTAATGTGACTATGCCAAAATCTAAAGATGAAGAAGGCTAGAAGAAATTTTGTCTGAGTGAAAGTTTATATGCTG
GTGTGGTCACTGACAGCTACAAATGAAAGTCCTAGAATTAATTATATTCAAATTGGTTTTCCTCCCTTGGTTAGTATTGC
TAGCAGAATGAATCAGACAACAGTAGCTACTGTCTTGGAATATCTGAGTAATTGGTTTGGAGAAAGAGACTTTACTTTGG
ATTTGAGAAGATGGCTTTATGTCTTATTGGCTTGCCTTGAAAAACCTTTATTACATGAGGTTCATTCACTGATTCAGCAG
CTTGCAAGAAGGTGCTCTGAAGTG

Alignment

ORF - retro_ptro_342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.91 %
• Parental protein coverage: 60.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLKRKQSVNISLSGCQPAPEGYSPTLQWQQQQVAQFST-VRQNVNKHRSHWKSQQLDSNVTMPKSEDEEG
          KLKRKQ.V..SL.GCQPAPEGYSP.LQWQ...VA.FST.VRQNV.KHRSHWKS.QLDSNVTMPKS.DEEG
Retrocopy KLKRKQGVKVSLLGCQPAPEGYSPILQWQ*K-VAPFST<VRQNVHKHRSHWKSRQLDSNVTMPKSKDEEG

Parental  WKKFCLGEKLCADGAVGPA-TNESPGIDYVQIGFPPLLSIVSRMNQATVTSVLEYLSNWFGERDFTPELG
          .KKFCL.E.L.A.G.V....TNESP.I.Y.QIGFPPL.SI.SRMNQ.TV..VLEYLSNWFGERDFT..L.
Retrocopy *KKFCLSESLYA-GVVTDS>TNESPRINYIQIGFPPLVSIASRMNQTTVATVLEYLSNWFGERDFTLDLR

Parental  RWLYALLACLEKPLLPEAHSLIRQLARRCSEV
          RWLY.LLACLEKPLL.E.HSLI.QLARRCSEV
Retrocopy RWLYVLLACLEKPLLHEVHSLIQQLARRCSEV

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	5.06 RPM
SRP007412_cerebellum	0.00 RPM	5.52 RPM
SRP007412_heart	0.00 RPM	2.71 RPM
SRP007412_kidney	0.00 RPM	3.69 RPM
SRP007412_liver	0.00 RPM	1.90 RPM
SRP007412_testis	0.21 RPM	9.70 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_342 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_342 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_455
Gorilla gorilla	retro_ggor_438
Pongo abelii	retro_pabe_278

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016248	1 retrocopy	retro_cjac_2630,
Dasypus novemcinctus	ENSDNOG00000018278	1 retrocopy	retro_dnov_1040,
Homo sapiens	ENSG00000092208	1 retrocopy	retro_hsap_455,
Gorilla gorilla	ENSGGOG00000016691	2 retrocopies	retro_ggor_1844, retro_ggor_438,
Microcebus murinus	ENSMICG00000004811	1 retrocopy	retro_mmur_1221,
Myotis lucifugus	ENSMLUG00000002619	1 retrocopy	retro_mluc_1005,
Mus musculus	ENSMUSG00000060121	1 retrocopy	retro_mmus_354,
Pongo abelii	ENSPPYG00000005764	1 retrocopy	retro_pabe_278,
Pan troglodytes	ENSPTRG00000006291	1 retrocopy	retro_ptro_342 ,