RetrogeneDB ID: retro_cjac_3182

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:11829358..11830678(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PES1
• Ensembl ID: ENSCJAG00000010617
• Aliases: None
• Description: None

Sequence

>retro_cjac_3182
ATGGGAGGCCTTGAGAAGAAGAAGTATGAACGAGGCTCAGCCACCAACTACATCACCCTGAACAAAGCCCGGAAGAAGCT
CCAGCTGAGCCTGGCTGACTTTAGGCGGCTGTGCATTCTGAAGGGCATTTATCCCCATGAACCCAAACACAAGAAGAAGG
TTAACAAGGGTTTTACAGCGGCCTGAACTTTTTACCTTATCAAAGACATCAGGTTTCTCCTCCATGAACCCATCGTCAAC
AAGTTCCGGGAATACAAGGTGTTCGTCCAGAAGCTCTGGAAGGCCTATGGGAAGAGCGAGTGGAACACCGTAGAGTGTCT
AAAGGACAATAAGCCCAACTACAAACTTGACCTCATCATCAAGGAACGGTACCCCACGTTCATTGATGCCCTGCGCGACC
TGGACGACGCCCTCTCCATGTGCTTCCTCTTTTCCACCTTCCCACGGACTGGCAAGTGTCACGTGCAGACCATTCAGCTG
TGCCGCCGGCTCACCGTGGAGTTCATGCATACATCATTGCCTCCTGTGCCCTGCGCAAGGTCTTCCTGTCCATCAAAGGC
ATTTACTACCAGGCCAAGGTGCTGGGGCAGCCCATCGTGTGGATCACTCCCTATGCCTTCTCCCATGACCACCCAACAGA
TGTGGACTACAGGGTCATGGCCACCTTCACTGAGTTCTACACCACCCTGCTGGGCTTCGTCAACTTCTGCCTCTACCAGT
TGCTCAACCTCCACTACCCCCCAAAGCTCGAGGGACAGGCCCCGGCAGAGGTGAAGGCCAGTGAGGACGCCTACGGCGCT
GGACTCTGAGAGCTCTATGGAGAAACTGGTGGCCCTCAGTGCCAGCCTGGCTCGTGTGGTGGTACCTGCCATGGAAGAGG
AGGCCGAGGTGGATGAGTTTCCTGCCGATGGGGAGATGTCGGCACAAGAGGAAGACCGCAGGAAGGAGCTGGAGGCGCAG
GAGAAGCACAAGAAGCTTTTTGAGGGCCTGACGTTCTTCCTGAACTGAGAGGTGCCCCGCGAGGCCCTGGCCTTCATCAT
CAGGAGTTTTGGGGGGAAAGGGTCCTGGGACAAATCTTTGTGCATTGGGGCCACCTACGACGTCACGGACTCCCGCATCA
CTCACCAGATTGTCGACCGGCCTGGGCAGCAGACCCCTGTCATAGGCAGGTGCTACATGCAGCCCCAGTGGGTGTTTGAC
TCAGTGAACGCTAGGCTCCTCCTCCCCGTGGCAGAGTACTTCCCTGGGGTGCAGCTCCCCCCACACCTTTCACCCTTTGT
GACTGAGAAGGAAGGAGATTATGTCCCACCTGACTGGCTC

Alignment

ORF - retro_cjac_3182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.8 %
• Parental protein coverage: 74.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGGLEKKKYERGSATNYITRNKARKKLQLSLADFRRLCILKGIYPHEPKHKKKVNKGSTAARTFYLIKDI
          MGGLEKKKYERGSATNYIT.NKARKKLQLSLADFRRLCILKGIYPHEPKHKKKVNKG.TAA.TFYLIKDI
Retrocopy MGGLEKKKYERGSATNYITLNKARKKLQLSLADFRRLCILKGIYPHEPKHKKKVNKGFTAA*TFYLIKDI

Parental  RFLLHEPIVNKFREYKVFVRKLRKAYGKSEWNTVERLKDNKPNYKLDHIIKERYPTFIDALRDLDDALSM
          RFLLHEPIVNKFREYKVFV.KL.KAYGKSEWNTVE.LKDNKPNYKLD.IIKERYPTFIDALRDLDDALSM
Retrocopy RFLLHEPIVNKFREYKVFVQKLWKAYGKSEWNTVECLKDNKPNYKLDLIIKERYPTFIDALRDLDDALSM

Parental  CFLFSTFPRTGKCHVQTIQLCRRLTVEFMH-YIIASRALRKVFLSIKGIYYQAEVLGQPIVWITPYAFSH
          CFLFSTFPRTGKCHVQTIQLCRRLTVEFMH.YIIAS.ALRKVFLSIKGIYYQA.VLGQPIVWITPYAFSH
Retrocopy CFLFSTFPRTGKCHVQTIQLCRRLTVEFMH<YIIASCALRKVFLSIKGIYYQAKVLGQPIVWITPYAFSH

Parental  DHPTDVDYRVMATFTEFYTTLLGFVNFRLYQSLNLHYPPKLEGQAQAEVKASEDTY-ALDSESSMEKLAA
          DHPTDVDYRVMATFTEFYTTLLGFVNF.LYQ.LNLHYPPKLEGQA.AEVKASED.Y.ALDSESSMEKL.A
Retrocopy DHPTDVDYRVMATFTEFYTTLLGFVNFCLYQLLNLHYPPKLEGQAPAEVKASEDAY>ALDSESSMEKLVA

Parental  LSASLARVVVPAMEEEAEVDEFPADGEMSAQEEDRRKELEAQEKHKKLFEGLKFFLNREVPREALAFIIR
          LSASLARVVVPAMEEEAEVDEFPADGEMSAQEEDRRKELEAQEKHKKLFEGL.FFLN.EVPREALAFIIR
Retrocopy LSASLARVVVPAMEEEAEVDEFPADGEMSAQEEDRRKELEAQEKHKKLFEGLTFFLN*EVPREALAFIIR

Parental  SFGGEVSWDKSLCIGATYDVTDSRITHQIVDRPGQQTPVIGRCYVQPQWVFDSVNARLLLPVAEYFPGVQ
          SFGG..SWDKSLCIGATYDVTDSRITHQIVDRPGQQTPVIGRCY.QPQWVFDSVNARLLLPVAEYFPGVQ
Retrocopy SFGGKGSWDKSLCIGATYDVTDSRITHQIVDRPGQQTPVIGRCYMQPQWVFDSVNARLLLPVAEYFPGVQ

Parental  LPPHLSPFVTEKEGDYVPPEKL
          LPPHLSPFVTEKEGDYVPP..L
Retrocopy LPPHLSPFVTEKEGDYVPPDWL

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	0.04 RPM	16.02 RPM
SRP051959_heart	0.02 RPM	14.54 RPM
SRP051959_kidney	0.02 RPM	23.10 RPM
SRP051959_liver	0.04 RPM	15.60 RPM
SRP051959_lung	0.02 RPM	17.10 RPM
SRP051959_lymph_node	0.02 RPM	17.42 RPM
SRP051959_skeletal_muscle	0.00 RPM	23.15 RPM
SRP051959_spleen	0.00 RPM	18.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3182 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3182 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3182 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010617	1 retrocopy	retro_cjac_3182 ,
Cavia porcellus	ENSCPOG00000003565	1 retrocopy	retro_cpor_986,
Homo sapiens	ENSG00000100029	1 retrocopy	retro_hsap_4133,
Otolemur garnettii	ENSOGAG00000005804	1 retrocopy	retro_ogar_1719,
Pongo abelii	ENSPPYG00000011716	1 retrocopy	retro_pabe_3471,
Pan troglodytes	ENSPTRG00000014251	2 retrocopies	retro_ptro_2018, retro_ptro_2809,
Rattus norvegicus	ENSRNOG00000004515	2 retrocopies	retro_rnor_2953, retro_rnor_824,
Tupaia belangeri	ENSTBEG00000009825	1 retrocopy	retro_tbel_1000,