RetrogeneDB ID: retro_ptro_883

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:99391127..99392546(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039913
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DUS1L
• Ensembl ID: ENSPTRG00000009790
• Aliases: None
• Description: None

Sequence

>retro_ptro_883
ATGCCAAAGCTGCAGGGCTTCGAGTTCTGGAGCCGCACCCTGCGAGGGGCCCGCCACGTCGTGGCCCCCATGGTGGACCA
GAGCGAGCTGGCCTGGAGGCTGCTGAGCCGGCGCCACGGGGCACAGCTCTGCTACACGCCCATGCTGCATGCCCAGGTCT
TTGTCCGCGACGCCAACTACCGGAAGGAGAACCTGTACTGCGAGGTGTGCCCCGAGGACCGGCCCCTCATCGTGCAGTTC
TGTGCCAATGACCCGGAGGTGTTTGTTCAGGCAGCTCTCCTGGCTCAGGATTACTGTGACGCCATTGACCTGAACTTGGG
CTGCCCACAGATGATAGCCAAGAGAGGTCACTATGGCGCCTTCCTGCAGGACGAGTGGGACCTGCTCCAAAGAATGATTT
TGCTGGCCCACGAGAAACTCTCTGTTCCTGTCACGTGCAAAATCCGTGTCTTCCCGGAGATTGACAAGACCATGAGGTAC
GCCCAGATGCTGGAGAAGGCCGGCTGCCAGTTGCTGACGGTGCACGGACGCACCAAAGAGCAGAAGGGGCCCCTGTCAGG
TGCAGCGTCCTGGGAGCATATCAAGGCTGTGCGGAAGGCTGTGGCCATCCCTGTGTTTGCTAATGGGAACATCCAGTGCC
TGCAGGATGTGGAGCGCTGCCTCCGGGACACGGGTGTGCAGGGCGTCATGAGCGCAGAGGGCAACCTACACAACCCCGCC
CTGTTCGAGGGCCGGAGCCCTGCCGTGTGGGAGCTGGCCGAGGAGTATCTGGACATCGTGCGGGAGCACCCCTGCCCGCT
GTCCTACGTCCGGGCCCACCTCTTCAAGCTGTGGCACCACACGCTGCAGGTGCACCAGGAGCTGCGAGAGGAGCTGGCCA
AGGTGAAGACCCTGGAGGGCATCGCTGCTGTGAGCCAGGAGCTGAAGCTGCGGTGTCAGGAGGAGATATCCAGGCAGGAG
GGAGCGAAGCCCACCGGCGATTTGCCCTTCCACTGGATCTGCCAGCCCTACATCCGGCCGGGGCCCAGGGAGGGGAGCAA
GGAGAAGGCGGGTGCGCGCAGCAAGCGGGCCCTGGAGGAAGAGGAGTGTGGCACGGAGGTCCTGTCCAAGAACAAGCAAA
AGAAGCAGCTGAGGAACCCCCACAAGACCTTCGACCCCTCTCTGAAGCCAAAATATGCAAAGTGTGACCAGTGTGGAAAC
CCAAAGGGCAACAGATGTGTGTTCAGCCTGTGCCGCGGCTGCTGCAAGAAGCGAGCCTCCAAAGAGACTGCAGACTGCCC
AGGTCACGGATTGCTTTTTAAAACCAAATTGGAGAAGTCTCTGGCCTGGAAAGAGGCCCAGCCTGAGCTGCAGGAGCCTC
AGCCAGCAGCACCTGGAACACCAGGTGGCTTCTCCGAAGTCATGGGCAGTGCCCTGGCC

Alignment

ORF - retro_ptro_883 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKLQGFEFWSRTLRGARHVVAPMVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYRKENLYCEVC
          MPKLQGFEFWSRTLRGARHVVAPMVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYRKENLYCEVC
Retrocopy MPKLQGFEFWSRTLRGARHVVAPMVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYRKENLYCEVC

Parental  PEDRPLIVQFCANDPEVFVQAALLAQDYCDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKL
          PEDRPLIVQFCANDPEVFVQAALLAQDYCDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKL
Retrocopy PEDRPLIVQFCANDPEVFVQAALLAQDYCDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKL

Parental  SVPVTCKIRVFPEIDKTVRYAQMLEKAGCQLLTVHGRTKEQKGPLSGAASWEHIKAVRKAVAIPVFANGN
          SVPVTCKIRVFPEIDKT.RYAQMLEKAGCQLLTVHGRTKEQKGPLSGAASWEHIKAVRKAVAIPVFANGN
Retrocopy SVPVTCKIRVFPEIDKTMRYAQMLEKAGCQLLTVHGRTKEQKGPLSGAASWEHIKAVRKAVAIPVFANGN

Parental  IQCLQDVERCLRDTGVQGVMSAEGNLHNPALFEGRSPAVWELAEEYLDIVREHPCPLSYVRAHLFKLWHH
          IQCLQDVERCLRDTGVQGVMSAEGNLHNPALFEGRSPAVWELAEEYLDIVREHPCPLSYVRAHLFKLWHH
Retrocopy IQCLQDVERCLRDTGVQGVMSAEGNLHNPALFEGRSPAVWELAEEYLDIVREHPCPLSYVRAHLFKLWHH

Parental  TLQVHQELREELAKVKTLEGIAAVSQELKLRCQEEISRQEGAKPTGDLPFHWICQPYIRPGPREGSKEKA
          TLQVHQELREELAKVKTLEGIAAVSQELKLRCQEEISRQEGAKPTGDLPFHWICQPYIRPGPREGSKEKA
Retrocopy TLQVHQELREELAKVKTLEGIAAVSQELKLRCQEEISRQEGAKPTGDLPFHWICQPYIRPGPREGSKEKA

Parental  GARSKRALEEEECGTEVLSKNKQKKQLRNPHKTFDPSLKPKYAKCDQCGNPKGNRCVFSLCRGCCKKRAS
          GARSKRALEEEECGTEVLSKNKQKKQLRNPHKTFDPSLKPKYAKCDQCGNPKGNRCVFSLCRGCCKKRAS
Retrocopy GARSKRALEEEECGTEVLSKNKQKKQLRNPHKTFDPSLKPKYAKCDQCGNPKGNRCVFSLCRGCCKKRAS

Parental  KETADCPGHGLLFKTKLEKSLAWKEAQPELQEPQPAAPGTPGGFSEVMGSALA
          KETADCPGHGLLFKTKLEKSLAWKEAQPELQEPQPAAPGTPGGFSEVMGSALA
Retrocopy KETADCPGHGLLFKTKLEKSLAWKEAQPELQEPQPAAPGTPGGFSEVMGSALA

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	1.98 RPM	34.19 RPM
SRP007412_cerebellum	0.29 RPM	19.32 RPM
SRP007412_heart	0.06 RPM	4.55 RPM
SRP007412_kidney	0.58 RPM	35.83 RPM
SRP007412_liver	1.08 RPM	23.67 RPM
SRP007412_testis	0.32 RPM	3.79 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_883 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_883 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018104	5 retrocopies	retro_cjac_1422, retro_cjac_1887, retro_cjac_3451, retro_cjac_4002, retro_cjac_4018,
Monodelphis domestica	ENSMODG00000003351	1 retrocopy	retro_mdom_1097,
Pan troglodytes	ENSPTRG00000009790	1 retrocopy	retro_ptro_883 ,