RetrogeneDB ID: retro_ptro_3261

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:116599525..116600747(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: API5
• Ensembl ID: ENSPTRG00000003516
• Aliases: None
• Description: None

Sequence

>retro_ptro_3261
ACTGGAGAAATCTTTCTCGAGTGGGCAGATATACTAACGCAACTTTTGCAGACAGATGACTCTGCAGAATTTAACCTAGT
GAACAATGCCCTGTTAAGTATATTTAAAATGGTTGCAAAAGGGACTTTAGGTGGGTTGTTCAGCCAAATACTTCAAGGAG
AGGACATTGTTAGAGAACGAGCAATTAAATTCCTTTCTACAAAACTTAAGACTTTACCAGATGAAGTCTTAACAAAGGAA
GTGAAAGAGCTTATATGAACTGAATCCAAAAAGGTCCTAGAAGATGTGACTGGTGAAGAATTTGTTCTATTATGAAAATA
CTGTCTGGGTTAAAAAGCTTACAGTGAGTGGAAGATAGCAACTTGTAGAGTTGGTGGCTGAACAGGCCGACCTAGAACAG
ACCTTCAATCCCTCGGATCCTGACTGTGTGTACAGGCTCTTACAGTGCACTTGGCAGGCAGTACCCCTCTTCTCTAGAAT
TATCCATTCCACAAGGTTTGTGACATATTTCTGTGAGCAGGTTCTCCCTAACCTCAGTACCTTGACTACCCCAGTGGAAG
GTCTTGATATACAGTTGGAGGTATTGAAATTGTTGGCTGAGATGAGTTCATTTTGTGGTGACAGGGAAAAACTGGAAACA
AATTTAAGAATACTATTTGATAAGTTATAGGAATACATGCCGCTCCCTCCAGAAGAAGCAGAAAATGGAGAGAATGCTGG
TAATGAAGAACCCAAGCTACAGTTCAGTTATGTGGAATGTTTGTTGTACAGTTTTCACTAGTTGGGCCGAAAACATCCAG
ATTTCTTAACAGCCAAACTGAATGCAGAAAAGCTCAAAGATTTCAAAATCAGGCTGCAATACTTTGCACGGGGCCTGCAA
ATTTATATCAGACAACTTCGCTTAGCTCTCCAGCTTAAAACGGGTGAGGCCTTAAAAACAGAAGAGAACGAGATTAAAGT
CGTTGCATTGAAAATAACAAACAATATCAATGCTTTAATCAAGGATCTCTTCCACATTCCTCCTTCTTATAAGAGCACAG
TAACACTATCCTGGAAACCTGTACAAAAGGTTGAGATTGGGCAAAAGAGAGCCAGTGAAGATACAACTTCAGGTTCACCA
CCCAAGAAATCTTCAGCAGGACCAAAAAGAGATACCAGGCAGATTTATAACCCTCCCAGTGGGAAATATAGCAGCAATTT
GAGCAACTTTAATTATGAGAGG

Alignment

ORF - retro_ptro_3261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.21 %
• Parental protein coverage: 78.05 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGENLPRVADILTQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQGEDIVRERAIKFLSTKLK
          TGE.....ADILTQLLQTDDSAEFNLVNNALLSIFKM.AKGTLGGLFSQILQGEDIVRERAIKFLSTKLK
Retrocopy TGEIFLEWADILTQLLQTDDSAEFNLVNNALLSIFKMVAKGTLGGLFSQILQGEDIVRERAIKFLSTKLK

Parental  TLPDEVLTKEVEELILTESKKVLEDVTGEEFVLF-MKILSGL-KSLQTVSGRQQLVELVAEQADLEQTFN
          TLPDEVLTKEV.ELI.TESKKVLEDVTGEEFVL..MKILSGL.K.L.TVSGR.QLVELVAEQADLEQTFN
Retrocopy TLPDEVLTKEVKELI*TESKKVLEDVTGEEFVLL<MKILSGL<KKL-TVSGR*QLVELVAEQADLEQTFN

Parental  PSDPDCVDRLLQCTRQAVPLFSKNVHSTRFVTYFCEQVLPNLGTLTTPVEGLDIQLEVLKLLAEMSSFCG
          PSDPDCV.RLLQCT.QAVPLFS...HSTRFVTYFCEQVLPNL.TLTTPVEGLDIQLEVLKLLAEMSSFCG
Retrocopy PSDPDCVYRLLQCTWQAVPLFSRIIHSTRFVTYFCEQVLPNLSTLTTPVEGLDIQLEVLKLLAEMSSFCG

Parental  DMEKLETNLRKLFDKLLEYMPLPPEEAENGENAGNEEPKLQFSYVECLLYSFHQLGRKLPDFLTAKLNAE
          D.EKLETNLR.LFDKL.EYMPLPPEEAENGENAGNEEPKLQFSYVECLLYSFH.LGRK.PDFLTAKLNAE
Retrocopy DREKLETNLRILFDKL*EYMPLPPEEAENGENAGNEEPKLQFSYVECLLYSFH*LGRKHPDFLTAKLNAE

Parental  KLKDFKIRLQYFARGLQVYIRQLRLALQGKTGEALKTEENKIKVVALKITNNINVLIKDLFHIPPSYKST
          KLKDFKIRLQYFARGLQ.YIRQLRLALQ.KTGEALKTEEN.IKVVALKITNNIN.LIKDLFHIPPSYKST
Retrocopy KLKDFKIRLQYFARGLQIYIRQLRLALQLKTGEALKTEENEIKVVALKITNNINALIKDLFHIPPSYKST

Parental  VTLSWKPVQKVEIGQKRASEDTTSGSPPKKSSAGPKRDARQIYNPPSGKYSSNLGNFNYEQ
          VTLSWKPVQKVEIGQKRASEDTTSGSPPKKSSAGPKRD.RQIYNPPSGKYSSNL.NFNYE.
Retrocopy VTLSWKPVQKVEIGQKRASEDTTSGSPPKKSSAGPKRDTRQIYNPPSGKYSSNLSNFNYER

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	0.11 RPM	22.09 RPM
SRP007412_cerebellum	0.29 RPM	44.45 RPM
SRP007412_heart	0.12 RPM	18.33 RPM
SRP007412_kidney	0.13 RPM	26.94 RPM
SRP007412_liver	0.16 RPM	19.31 RPM
SRP007412_testis	0.00 RPM	29.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3261 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3261 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3261 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4893
Gorilla gorilla	retro_ggor_3055
Pongo abelii	retro_pabe_3805

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000166181	2 retrocopies	retro_hsap_2350, retro_hsap_4893,
Gorilla gorilla	ENSGGOG00000002358	2 retrocopies	retro_ggor_1784, retro_ggor_3055,
Myotis lucifugus	ENSMLUG00000013546	1 retrocopy	retro_mluc_245,
Nomascus leucogenys	ENSNLEG00000017956	1 retrocopy	retro_nleu_352,
Pan troglodytes	ENSPTRG00000003516	2 retrocopies	retro_ptro_1720, retro_ptro_3261 ,