RetrogeneDB ID: retro_cjac_1499

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:19312693..19313975(-)
• Located in intron of: ENSCJAG00000004616

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF3
• Ensembl ID: ENSCJAG00000009926
• Aliases: None
• Description: None

Sequence

>retro_cjac_1499
TCAGGAGTAAAGAAGCGACGAATACCCCATTTTGAGGAGGTGGAAGAAGAGTCAGAGGTGATCCCTGGGTCTCCATCAGA
GAGCCCTGGCATGCTGACTAAGCTCCAGATCAAACAGATGATGGAGCAGCAACACGACACATCGAGGAGAGGAAAAAACA
GCTGAGCTTCATTAGCCCCTGTACATCTCAGCCAAAGACTCCTTCTTCCTCCCAACCAGAGTGACTTCCAATTGGCAACA
CTATTCAGCCCTTCTAGACTGCCACTTTCATGAATGATGCCATTGAGAAGGCAAGGAAAGCAGCTGAACTACAAGCTCAT
ATCCAAGCCCGGCTGGCACTGAAGCCAGGACTCATCAGTAATGCCAACATGGTGGGTCTGGCTAATCTCCATGCCATAGG
CATTGCTCCCCTGAAGATGGAGTTAAAAGACCAAATTAAACCTGCACCACTGATCCTAGATGAGCAAGGCACACTGTAGA
TGCAATAGGCAATGAGATTGAGCTGACACACTGCATCCCTACTCTGAAGGCCAATATTCGTGCTGTGAAGAGGGAACCAT
TGCAGCAACAGCTAAAATAAAAGCCATCAGAAGACATGGAGTCCAATACCTTTTTTGACCCCTGAGTCTCCATTGCCTCT
TCTCAGAGACAGAGATGCAGTTTTAAATTCCATGACAAAGGCAAATTTGCAAAGATTGCTCAGCGATTAAGGACAAAGGC
TCAACTGGAGAAGCTATAGGAGAGATTTCACAAGTAGCTCAAAAAACAGGCTTCCATACTTCAACTAGGCTTGCCCTCAT
TGCTCCTAAGAAGAAGCTAAAGGAAGGAGATATCCCTGAAATTGAGTGGTGGGACTCATATAATCCCCAGTGGCTTTGAC
CTTACAGAGGAAAATCCCAAGAGACCAGATTATTTTGGAATCACAAATCTTGTTAAACATCCAGCCCAGCTCAATCCTCC
AGTCAACAATGACACACCAGTTATTCTGGGAGTATATCTTAACAAGAAGGAACAGAAATAAATTCGGAGACAAACAAGGA
GGGAAGCACAGAAGAAACTACCAGAATAAGTCATGCTGGGCCTGATGCCTCCTCCAGAACCCAAAGTGAGAATTTCTAAT
TTGATGCAAGAATTAGGAACAGAAGCTGTTCAAGACCCCACGAAGGTAGAAGCCCATGTCAGAGCTCAGATGGCAAAAAG
ACAGAAAATGCATGAAGAGGCCAACACTACCTGAAAACTCATAGCAGAACAGAGAAAGGTCAAGAAAATTAAAAAGTTTA
AG

Alignment

ORF - retro_cjac_1499 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.56 %
• Parental protein coverage: 62.87 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SGVKKRRIPRFEEVEEEPEVIPGPPSESPGMLTKLQIKQMME-AATRQIEERKKQLSFISPPTPQPKTPS
          SGVKKRRIP.FEEVEEE.EVIPG.PSESPGMLTKLQIKQMME.AATR.IEERKKQLSFISP.T.QPKTPS
Retrocopy SGVKKRRIPHFEEVEEESEVIPGSPSESPGMLTKLQIKQMME<AATRHIEERKKQLSFISPCTSQPKTPS

Parental  SSQPERLPIGNTIQPSQAATFMNDAIEKARKAAELQARIQAQLALKPGLIGNANMVGLANLHAMGIAPPK
          SSQPE.LPIGNTIQP...ATFMNDAIEKARKAAELQA.IQA.LALKPGLI.NANMVGLANLHA.GIAP.K
Retrocopy SSQPE*LPIGNTIQPF*TATFMNDAIEKARKAAELQAHIQARLALKPGLISNANMVGLANLHAIGIAPLK

Parental  VELKDQTKPTPLILDEQG-RTVDATGKEIELTHRMPTLKANIRAVKREQFKQQLKEKPSEDMESNTFFDP
          .ELKDQ.KP.PLILDEQG..TVDA.G.EIELTH..PTLKANIRAVKRE...QQLK.KPSEDMESNTFFDP
Retrocopy MELKDQIKPAPLILDEQG<HTVDAIGNEIELTHCIPTLKANIRAVKREPLQQQLK*KPSEDMESNTFFDP

Parental  RVSIAPSQRQRRTFKFHDKGKFEKIAQRLRTKAQLEKL-QAEISQAARKTGIHTSTRLALIAPKKELKEG
          .VSIA.SQRQR..FKFHDKGKF.KIAQRLRTKAQLEKL...EISQ.A.KTG.HTSTRLALIAPKK.LKEG
Retrocopy *VSIASSQRQRCSFKFHDKGKFAKIAQRLRTKAQLEKL<IGEISQVAQKTGFHTSTRLALIAPKKKLKEG

Parental  DIPEIEWW-DSYIIPNGFDLTEENPKREDYFGITNLVEHPAQLNPPVDNDTPVTLGVYLTKKEQKKLRRQ
          DIPEIE.W....IIP.GFDLTEENPKR.DYFGITNLV.HPAQLNPPV.NDTPV.LGVYL.KKEQK..RRQ
Retrocopy DIPEIE-W>GTHIIPSGFDLTEENPKRPDYFGITNLVKHPAQLNPPVNNDTPVILGVYLNKKEQK*IRRQ

Parental  TRREAQKELQEKVRLGLMPPPEPKXVRISNLMRVLGTEAVQDPTKVEAHVRAQMAKRQKAHEEANAARKL
          TRREAQK.L.E.V.LGLMPPPEPK.VRISNLM..LGTEAVQDPTKVEAHVRAQMAKRQK.HEEAN...KL
Retrocopy TRREAQKKLPE*VMLGLMPPPEPK-VRISNLMQELGTEAVQDPTKVEAHVRAQMAKRQKMHEEANTT*KL

Parental  TAEQRKVKKIKKLK
          .AEQRKVKKIKK.K
Retrocopy IAEQRKVKKIKKFK

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	0.02 RPM	18.57 RPM
SRP051959_heart	0.00 RPM	19.94 RPM
SRP051959_kidney	0.00 RPM	22.03 RPM
SRP051959_liver	0.00 RPM	22.53 RPM
SRP051959_lung	0.00 RPM	33.25 RPM
SRP051959_lymph_node	0.00 RPM	35.41 RPM
SRP051959_skeletal_muscle	0.00 RPM	20.05 RPM
SRP051959_spleen	0.00 RPM	31.60 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1499 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1499 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1499 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4069
Pan troglodytes	retro_ptro_2758
Macaca mulatta	retro_mmul_2348

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009926	1 retrocopy	retro_cjac_1499 ,
Macaca mulatta	ENSMMUG00000016301	1 retrocopy	retro_mmul_2348,
Nomascus leucogenys	ENSNLEG00000009841	1 retrocopy	retro_nleu_2529,
Otolemur garnettii	ENSOGAG00000005352	4 retrocopies	retro_ogar_2360, retro_ogar_3052, retro_ogar_374, retro_ogar_409,
Pan troglodytes	ENSPTRG00000001254	1 retrocopy	retro_ptro_2758,