RetrogeneDB ID: retro_ptro_3279

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:156076430..156077168(-)
• Located in intron of: ENSPTRG00000022462

Retrocopy information

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

Parental gene information

• Parental gene symbol: TWF1
• Ensembl ID: ENSPTRG00000004846
• Aliases: TWF1, PTK9
• Description: None

Sequence

>retro_ptro_3279
TATAGTCAGCCTTCAGATTCCTGGGATAAGGATTATGATTCCTTTGTTTTACCCCTGTTGGAGGACAAACAACTGTGCTA
TATATTATTCAGGTTAGATTCTCAGAATGCCCAGGGATATGAATGGATATTCATTGCATGGTTTCCAGATCATTCTCATG
TCCGTCAAAAAAGGTTATATGCAGCAACAAGAGCAACTCTGGAAAAGGAATCTGGAGGTGGCCACGTTAAAGATGAAGTA
TTTGGAACAGTAAAGGAAGATGTATCATTACATGGATATAAAAAATGTTTGCTCTCACAATCTTCCCCTGCCCCACTGAC
TGCAGCTGAGGAAAAATTATGACATTAAAATCAATGAGGTACAGACTGACGTGGGTGTGGACGCTAAGCATCAAACACTA
CAAGGAGTAGCATTTCCTATTTCTCGAGAAGCTTTTCAGGCTTTGGAAAAAATAAATAACAGCTGAACTATGTGCAGTTG
GAAATAAACATAAAAAATGAAATTATAATTTTGGCCAACACAACAAATACAGAACTAAAAGATTTGCCAAAGAGGATTCC
CAAGGATTCAGCTCATTACCATTTCTTTCTGTATAAACATTCCCATGAAGGAGACTATTTAGAGTCCATAGTTTTTATCT
ATTCAATGCCCAGATACACATGCAGTATAAGAGAACGGATGCTGTATTCTAGCTGCAAGAGCCCTCTGCTAGAAATTGTA
GAAAGACAACTATGGATG

Alignment

ORF - retro_ptro_3279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.6 %
• Parental protein coverage: 64.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YSQPSDSWDKDYDSFVLPLLEDKQPCYILFRLDSQNAQGYEWIFIAWSPDHSHVRQKMLYAATRATLKKE
          YSQPSDSWDKDYDSFVLPLLEDKQ.CYILFRLDSQNAQGYEWIFIAW.PDHSHVRQK.LYAATRATL.KE
Retrocopy YSQPSDSWDKDYDSFVLPLLEDKQLCYILFRLDSQNAQGYEWIFIAWFPDHSHVRQKRLYAATRATLEKE

Parental  FGGGHIKDEVFGTVKEDVSLHGYKKYLLSQSSPAPLTAAEEELR-QIKINEVQTDVGVDTKHQTLQGVAF
          .GGGH.KDEVFGTVKEDVSLHGYKK.LLSQSSPAPLT.A.EE....IKINEVQTDVGVD.KHQTLQGVAF
Retrocopy SGGGHVKDEVFGTVKEDVSLHGYKKCLLSQSSPAPLT-AAEEKL>DIKINEVQTDVGVDAKHQTLQGVAF

Parental  PISREA-FQALEKLNNRQLNYVQLEIDIKNEIIILANTTNTELKDLPKRIPKDSARYHFFLYKHSHEGDY
          PISREA.F....K.N..QLNYVQLEI.IKNEIIILANTTNTELKDLPKRIPKDSA.YHFFLYKHSHEGDY
Retrocopy PISREA<FSGFGK-NK*QLNYVQLEINIKNEIIILANTTNTELKDLPKRIPKDSAHYHFFLYKHSHEGDY

Parental  LESIVFIYSMPGYTCSIRERMLYSSCKSPLLEIVERQLQM
          LESIVFIYSMP.YTCSIRERMLYSSCKSPLLEIVERQL.M
Retrocopy LESIVFIYSMPRYTCSIRERMLYSSCKSPLLEIVERQLWM

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	0.02 RPM	15.78 RPM
SRP007412_cerebellum	0.00 RPM	13.01 RPM
SRP007412_heart	0.06 RPM	7.37 RPM
SRP007412_kidney	0.00 RPM	36.17 RPM
SRP007412_liver	0.00 RPM	22.23 RPM
SRP007412_testis	0.00 RPM	14.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3279 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3279 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3279 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4916

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017332	1 retrocopy	retro_amel_1224,
Choloepus hoffmanni	ENSCHOG00000008386	5 retrocopies	retro_chof_1525, retro_chof_2013, retro_chof_2569, retro_chof_391, retro_chof_509,
Homo sapiens	ENSG00000151239	2 retrocopies	retro_hsap_1819, retro_hsap_4916,
Monodelphis domestica	ENSMODG00000018535	1 retrocopy	retro_mdom_167,
Mustela putorius furo	ENSMPUG00000000364	1 retrocopy	retro_mputfur_1629,
Mus musculus	ENSMUSG00000022451	1 retrocopy	retro_mmus_2961,
Nomascus leucogenys	ENSNLEG00000017931	1 retrocopy	retro_nleu_2877,
Otolemur garnettii	ENSOGAG00000007525	1 retrocopy	retro_ogar_1058,
Pan troglodytes	ENSPTRG00000004846	1 retrocopy	retro_ptro_3279 ,
Rattus norvegicus	ENSRNOG00000022507	1 retrocopy	retro_rnor_2176,