RetrogeneDB ID: retro_ptro_576

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:111701414..111702053(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3GL2
• Ensembl ID: ENSPTRG00000020792
• Aliases: None
• Description: SH3-domain GRB2-like 2 [Source:HGNC Symbol;Acc:10831]

Sequence

>retro_ptro_576
CTTCAAAGAGATGGAGATGTCATCAGCAAGGCGGTGACGGAAATGCTGGCAAGGACCATCAAGTACCTGCAGCCCAACCC
AGCCTCACAGGCTAAGCTGACCATGCTCAACGCGGTGTGCAAGATCCGGGGCCAGGTGAAGAACCCCGGCTACCCGCAGT
CGGAGGGGCTCCTGAGCGAGTGCCTGATCCGCCACCAGAAGGAGCTGCGCAACGAGTCCAACTTCAGTGACGCACTGCTG
GATGCCGGCGAGTCCATGAAGCACCTGGCAGAGGTGAAGGACTCCCTGGACATAGAGGTCAAGCAGAACTTCATTGACCT
CCTCCAGAACCTGTGTGAGAAAGACCTGAAGGAGATCCAGCACCACCTGTAGAAGCTGGAGGGCCGCCGCCTGGACTTAG
ACTAAAAGAAGCGGCAGGACAAGATCCCCGATGAGGAGCTGCGCCAGGCGCTGGAGAAGTTTGAGGACTCCAAGGAGGTA
GCAGAAACCAGCATGCGCAACCTCCTGGACACCGACATTGGGCAGGTGAGTCAACTCCCGGTCCTGGTGGAGGCGCAGCT
GTACTACCACTGGCAGGCCTTGCAGATCCTAGACGAGCTGGCAGCGAAGCTCAAGCGCAGGATGCGGAAATCTTCCTCA

Alignment

ORF - retro_ptro_576 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.02 %
• Parental protein coverage: 60.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MERKVDVTSRAVMEIMTKTIEYLQPNPASRAKLSMINTMSKIRGQEKGPGYPQAEALLAEAMLKFGRELG
          ..R..DV.S.AV.E....TI.YLQPNPAS.AKL.M.N...KIRGQ.K.PGYPQ.E.LL.E.......EL.
Retrocopy LQRDGDVISKAVTEMLARTIKYLQPNPASQAKLTMLNAVCKIRGQVKNPGYPQSEGLLSECLIRHQKELR

Parental  DDCNFGPALGEVGEAMRELSEVKDSLDIEVKQNFIDPLQNLHDKDLREIQHHLKKLEGRRLDFDYKKKRQ
          ...NF..AL...GE.M..L.EVKDSLDIEVKQNFID.LQNL..KDL.EIQHHL.KLEGRRLD.D..KKRQ
Retrocopy NESNFSDALLDAGESMKHLAEVKDSLDIEVKQNFIDLLQNLCEKDLKEIQHHL*KLEGRRLDLD-*KKRQ

Parental  GKIPDEELRQALEKFDESKEIAESSMFNLLEMDIEQVSQLSALVQAQLEYHKQAVQILQQVTVRLEERIR
          .KIPDEELRQALEKF..SKE.AE.SM.NLL..DI.QVSQL..LV.AQL.YH.QA.QIL......L..R.R
Retrocopy DKIPDEELRQALEKFEDSKEVAETSMRNLLDTDIGQVSQLPVLVEAQLYYHWQALQILDELAAKLKRRMR

Parental  QASS
          ..SS
Retrocopy KSSS

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	0.14 RPM	191.47 RPM
SRP007412_cerebellum	0.32 RPM	262.52 RPM
SRP007412_heart	0.09 RPM	22.27 RPM
SRP007412_kidney	0.47 RPM	34.00 RPM
SRP007412_liver	0.29 RPM	0.07 RPM
SRP007412_testis	4.64 RPM	8.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_576 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_576 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_576 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_675

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010823	1 retrocopy	retro_amel_1668,
Choloepus hoffmanni	ENSCHOG00000001689	2 retrocopies	retro_chof_1007, retro_chof_24,
Macropus eugenii	ENSMEUG00000015197	1 retrocopy	retro_meug_523,
Macaca mulatta	ENSMMUG00000000273	1 retrocopy	retro_mmul_1264,
Pan troglodytes	ENSPTRG00000020792	1 retrocopy	retro_ptro_576 ,