RetrogeneDB ID: retro_cjac_1887

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:16204021..16205437(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032860
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DUS1L
• Ensembl ID: ENSCJAG00000018104
• Aliases: None
• Description: None

Sequence

>retro_cjac_1887
ATGCCAAAGCTGCAGGGCTTCGAGTTCTGGAGTCACACCCTCCGGGAGGCCCGCCACGTGGTGGCCCCCAAGGTGGACCA
GAGCGAGCTGGCCTGGAGACTGCTAAGCCGGCTCCACGGGGCACAGCTCTGCTACACGCCCATGCTGCACGCCCAAGTCT
TCGTCCGCGACACCAACTACCGGAAGGAGAACCTGTACTGCAAGGTGTGCCCTGAGGATCGGCCCCTCATCGTACAGTTC
TGCGCCAATGACCCGGAGGTGTTTGTTCAGGTGGCTCTCCTGGCTCAGGATTACTGTGACGCCATCGACCTGAACCTGGG
CTACCCACAGATGATAGTCAAGAGAGGTCACTATGGCGCCTTCCTGCAGGACCAGTGGGACCTGCTCCAAAGAATGATTT
TGCTGGCCCACGAGAAACTCTCTGTTCCCGTCACGTGCAAAATCCGTGTCTTCCCAGAGATTGACAAGACGGTGAGGTAT
GCCCAGATGCTGGAGAAGGCCGGCTGCCAGTTGCTGACCGTGCATGGGCGCACCAAGGAGCAGAAGGGGCCCCTGTCGGG
TGTGGCGTCCTGGAAGCACATCAGGGCCATGTGGAAAGCTGTGGCCATCCCTGTGTTTGCCAATGGAAACATCCAGAGCC
TACAGGGATGTGGAGCGCTGTATCCAGGACACCGGTGTACAGGGTGTCATGAGCTCAGAAGGCAACCTGCACAATCCCGC
CGTGTTTGAGGGCCGGAGCCCTGCCGTGTGGGAGCTGGCCGAGGAATACCTGGACATCGTGCGGGAGCACCCCTGCCCGC
TGTCCTACGTCCGGGCCCACCTCTGCAAGCTGTGGCACCACACGCTGCAGGTGCATCAGCAGCTGTGAGAGGAGCTGGCC
AAGGTGAAGACCCTCGAGGGCATTGCTGCCGTGAGCCAGGAGCTGAAGATGCGGTGTCAGGAGGAGATATCCAGGCAGGA
GGGAGCGAAGCCCGCCGGCGACTTGCCCTTCCACTGGATTTGCCAGCCCTACGTCCGGCCGGGGCCCAGGGAGGGGAGCA
AGGAGAAGGCAGGTGGGCTCAACAAGCGGGCCCTGGAGGAGGAGTGTGGCACGCAAGTCCTGTCCGAGAACAAGCCTAAG
CAGCAGCTGAGGAACCCCCACAAGACCTTCGACCCCTCTCTGAAGCCAAAATATGCAAAATGTGACCAGTGTGGAAACCC
AAAGGGCAACAGATGTGTGTTCAGCCTGTGCGAGGCTGCTGCAAGAAGCGAGCCTCCAAAGAGACTGCGGACTGCCCAGG
TCACGGATTGCTTTTCAAAGCCAAATTGGAGAAGTCTCTGGCCGGGAAACGGACCCAGCCTGAGCTGCAGGAGCCTCAGA
CGGCCCCGCCCGGCACACCAGGGGGCTTCTCAGAAGTCATGAGTAGTGCTCTGGCC

Alignment

ORF - retro_cjac_1887 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKLQGFEFWSHTLRGARHVVAPMVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYRKENLYCEVC
          MPKLQGFEFWSHTLR.ARHVVAP.VDQSELAWRLLSR.HGAQLCYTPMLHAQVFVRD.NYRKENLYC.VC
Retrocopy MPKLQGFEFWSHTLREARHVVAPKVDQSELAWRLLSRLHGAQLCYTPMLHAQVFVRDTNYRKENLYCKVC

Parental  PEDRPLIVQFCANDPEVFVQVALLVQGYCDAIDMNPGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKL
          PEDRPLIVQFCANDPEVFVQVALL.Q.YCDAID.N.G.PQMI.KRGHYGAFLQD.WDLLQRMILLAHEKL
Retrocopy PEDRPLIVQFCANDPEVFVQVALLAQDYCDAIDLNLGYPQMIVKRGHYGAFLQDQWDLLQRMILLAHEKL

Parental  SVPVTCKILVFPEIDKTVRYAQMLEKAGCQLLIVHGCTKQQKVPLSSAASWEHIKAVRKAVAIPVFANGN
          SVPVTCKI.VFPEIDKTVRYAQMLEKAGCQLL.VHG.TK.QK.PLS..ASW.HI.A..KAVAIPVFANGN
Retrocopy SVPVTCKIRVFPEIDKTVRYAQMLEKAGCQLLTVHGRTKEQKGPLSGVASWKHIRAMWKAVAIPVFANGN

Parental  IQSLQ-DVERCIQDTGVQGVMSAEGNLHNPALFEGRSPAVWELAEEYLDIVREHPCPLSYVRAHLFKLWH
          IQSLQ.DVERCIQDTGVQGVMS.EGNLHNPA.FEGRSPAVWELAEEYLDIVREHPCPLSYVRAHL.KLWH
Retrocopy IQSLQ>DVERCIQDTGVQGVMSSEGNLHNPAVFEGRSPAVWELAEEYLDIVREHPCPLSYVRAHLCKLWH

Parental  HTLQVHQQLREELAKVKTLEGIAAVSQELKMRCQEEISRQEGAKPTGNLPFHWICQPYVRPGPRERSKEK
          HTLQVHQQL.EELAKVKTLEGIAAVSQELKMRCQEEISRQEGAKP.G.LPFHWICQPYVRPGPRE.SKEK
Retrocopy HTLQVHQQL*EELAKVKTLEGIAAVSQELKMRCQEEISRQEGAKPAGDLPFHWICQPYVRPGPREGSKEK

Parental  AGARSKRALEEEEECGTEVLSKNKQKKQLRNPHKTFDPSLKPKYAKCDQCGNPKGNRCVFSLC-RGCCKR
          AG...KRAL..EEECGT.VLS.NK.K.QLRNPHKTFDPSLKPKYAKCDQCGNPKGNRCVFSLC.RGCCK.
Retrocopy AGGLNKRAL--EEECGTQVLSENKPKQQLRNPHKTFDPSLKPKYAKCDQCGNPKGNRCVFSLC<RGCCKK

Parental  RASKETADCPGHGLLFKTKLEKSLIWKGTQPELQEPQTATPGTPGGFSEVMSSALA
          RASKETADCPGHGLLFK.KLEKSL..K.TQPELQEPQTA.PGTPGGFSEVMSSALA
Retrocopy RASKETADCPGHGLLFKAKLEKSLAGKRTQPELQEPQTAPPGTPGGFSEVMSSALA

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
SRP051959_colon	0.11 RPM	12.31 RPM
SRP051959_heart	0.09 RPM	10.26 RPM
SRP051959_kidney	0.09 RPM	15.29 RPM
SRP051959_liver	0.15 RPM	24.11 RPM
SRP051959_lung	0.11 RPM	11.26 RPM
SRP051959_lymph_node	0.09 RPM	12.15 RPM
SRP051959_skeletal_muscle	0.11 RPM	30.97 RPM
SRP051959_spleen	0.15 RPM	12.16 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1887 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1887 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1887 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,