RetrogeneDB ID: retro_cjac_916

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:59611397..59613252(-)
• Located in intron of: ENSCJAG00000014753

Retrocopy information

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

Parental gene information

• Parental gene symbol: NCOA4
• Ensembl ID: ENSCJAG00000013352
• Aliases: None
• Description: None

Sequence

>retro_cjac_916
ATGAATACCTTCCAAGACCAGAGTGGCAGCTCCAATAATAAAGAACCCCTTTTGAGGTGTAGTGATGCACGGAGGGACCT
GGAGCTTGCTATTGGTGGAGTTCTCTGGACTGAGCAGCAAATTAAAGATAACTTGCGAGAGGTCAAACCTTAGATTCACG
GTTGCATAAGCCATCACCTGGAATGCCTTAGAAGCCGTGAGGTGTGGCTATATGAACAGGTGGACCTCATCTATCAGCTT
AAAGAGGAGATACTTCGGCAGCAAGCTCAGCAGCTGTACTGGTTATTGGGCCAGTTCAACTGTCTTACTCATTAACTGGA
GTGTACCCAAAACAGAGATCTAGCCAAACAAGTCTCCGTGTGCCTGGAGAGACTGGGCAGTTTGACCCTCAAGCCTGAAA
ATTCAACTGTCCTGCTCTTTGAAGCCGACACAACTGCTCTGCACCAGACCATCACCACCTTTGGGTCTCTCAAAACCATT
CAAATTCCTGAGCACTTGATGGCTCATGCTAGTTTATCAAATATCGGGCCCTTCCTGGAGAAGAGAGGCTATATCCCAAT
GCCAGAGCAGAAGCGAGCATCCGTATTGCAACTGTCCCTCTCAGCGAATGGCACCTTGGAAGCAAACCTGCCAGTTGTCA
TCAGGCTCCTTACATACCCAGCACCAACCCCCAGGACTGGCTCATCCAAAAGCAGACCTTAGAGAATAGTCAGACTTCTT
CCAGAACTGCAATTTCTTCAGTAATGTCTGGGGAAACCTAAAGGACTTAGAAAACTGGCTCCTCAAGAGTCAGCAACAGG
AAATTCCGGAAAAACCAAGTTATCAAAAGTGTAACAGCCATTCCACTACTAGTTCTTTCTCCACTGAAATGAAAAAGGTT
GAAGATCTAGAGCTTCCTGATCAACATAAGATGGACTTATCAGATTGGCTGGTGACTCCCCAGGAATCCCATAAGCTGGG
GAAGCCTGAGAATGGCAGTCATTAAATCAGTGAGAAGTTTAAGCTCTTGTTCCAGTCCTACAATGTGAATGATTGGCTTG
TCAAGACTGACTCCTGTACCAACTGTCAGGGAAACCAGCCCAAAGGTATGGAGATTGAAAACCTGGGCAATCTGAAGTGC
CTAAATGACTACTTGGAGGCCAAGAAACCATTGTCCACCCCCAGGGTGGTTACAGAGGATTGGCTTGTCTAGAACCATCA
CAACCCATGTAAGGTAGAGGAGGTGTACAGAGCCAATGAACCCTGCACAAGGTTTGCAGAGTGCGTGTGTGATGAGCATT
GTGAGAAGGAGGCTCTGTATAAATGGCTTCTGAAGAAAGAAGGAAAGGATAAAAATGGGATGCCCATGGAACCCAAACCT
GAGAAGCATAAAGATTCCCTGAATATGTGGCTCTGTCCTTCTAGAAAAGAAGTAATAGAACAACCTAAAGCACCAAAGGC
AATGGTTCCTTCTAGAATTGCTGATTCCTTCCAAGTCATAAAGAACAGCCCCTTGTCGGAGTGGCTTATCAGGCCCCTAT
ACAAAGAAGGAAGTCCCAAGGAAGTGCCTAGTACTGAAGACAGAGCTGGCAAACAAAAGCTTAAAAGGCTGATGAGCACT
TTCTGGTGTTCCATTAACACAGCAGACTGGGTCCTGCCAGGAAAGAAGATGGGCAACCTCAGCCAGTTATCCTCTGGAGA
AGACAAGTGTAAGATTCAAAAGAAGGCCCAGAAGAAGTACTACTTAATTCACCTCTACAGGAGGAACATAAGTTCCCCCC
AGACCATTACGGTCTCCCTGCAGTTTGTGATCTCTGCCTGCATGCAGCTTAAAGTTGATAAAGAGAAGTGGTTATATTGA
ACTCCTCTACAGATG

Alignment

ORF - retro_cjac_916 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.52 %
• Parental protein coverage: 94.81 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNTFQDQSGSSSNREPLLRCSDARRDLELAIGGVLRAEQQIKDNLREVKAQIHSCISRHLECLRSREVWL
          MNTFQDQSGSS.N.EPLLRCSDARRDLELAIGGVL..EQQIKDNLREVK..IH.CIS.HLECLRSREVWL
Retrocopy MNTFQDQSGSSNNKEPLLRCSDARRDLELAIGGVLWTEQQIKDNLREVKP*IHGCISHHLECLRSREVWL

Parental  YEQVDLIYQLKEETLQQQAQQLYWLLGQFNCLTHQLECTQNKDLANQVSVCLERLGSLTLKPEDSTVLLF
          YEQVDLIYQLKEE.L.QQAQQLYWLLGQFNCLTH.LECTQN.DLA.QVSVCLERLGSLTLKPE.STVLLF
Retrocopy YEQVDLIYQLKEEILRQQAQQLYWLLGQFNCLTH*LECTQNRDLAKQVSVCLERLGSLTLKPENSTVLLF

Parental  EADTTALRQTITTFGSLKTIQIPEHLMAHASSSNIGPFLEKRGYIPMPEQKSAS-SIAAVPLSEWLLGSK
          EADTTAL.QTITTFGSLKTIQIPEHLMAHAS.SNIGPFLEKRGYIPMPEQK.AS..IA.VPLSEW.LGSK
Retrocopy EADTTALHQTITTFGSLKTIQIPEHLMAHASLSNIGPFLEKRGYIPMPEQKRAS<RIATVPLSEWHLGSK

Parental  PASGSQAPYISSTNPQDWLTQKQTLENSQTSSRA-CNFFSNVWGNLKDLENWLLKSQQQEVPEKPSYQKC
          PAS..QAPYI.STNPQDWL.QKQTLENSQTSSR..CNFFSNVWGNLKDLENWLLKSQQQE.PEKPSYQKC
Retrocopy PASCHQAPYIPSTNPQDWLIQKQTLENSQTSSRT<CNFFSNVWGNLKDLENWLLKSQQQEIPEKPSYQKC

Parental  NSHSTAGSFSTEMEKVEDLELPDQDKMDLSDWLVTPQESHKLGKPENGSHEISEKFKLLFQSYNVNDWLV
          NSHST..SFSTEM.KVEDLELPDQ.KMDLSDWLVTPQESHKLGKPENGSH.ISEKFKLLFQSYNVNDWLV
Retrocopy NSHSTTSSFSTEMKKVEDLELPDQHKMDLSDWLVTPQESHKLGKPENGSH*ISEKFKLLFQSYNVNDWLV

Parental  KTDSCTNCQGNQPKGVEIENLGNLKCLNDHLEAKKPLSTTSVVTEDWLVQNRQDPCKVEEVCRANEPCTS
          KTDSCTNCQGNQPKG.EIENLGNLKCLND.LEAKKPLST..VVTEDWLV.N...PCKVEEV.RANEPCT.
Retrocopy KTDSCTNCQGNQPKGMEIENLGNLKCLNDYLEAKKPLSTPRVVTEDWLV*NHHNPCKVEEVYRANEPCTR

Parental  FAECVCDENCEKEALYKWLLKKEGKDKNGMPMEPKPEPEKHKDSLNMWLCPSRKEVIEQPKAPKAMVPSR
          FAECVCDE.CEKEALYKWLLKKEGKDKNGMPMEPK..PEKHKDSLNMWLCPSRKEVIEQPKAPKAMVPSR
Retrocopy FAECVCDEHCEKEALYKWLLKKEGKDKNGMPMEPK--PEKHKDSLNMWLCPSRKEVIEQPKAPKAMVPSR

Parental  IADSFQVIKNSPLSEWLIRPLNKEGSPKEVPSTEDRAGKQKLKSPMSTFWCPFNTADWVLPGKKMGNVSQ
          IADSFQVIKNSPLSEWLIRPL.KEGSPKEVPSTEDRAGKQKLK..MSTFWC..NTADWVLPGKKMGN.SQ
Retrocopy IADSFQVIKNSPLSEWLIRPLYKEGSPKEVPSTEDRAGKQKLKRLMSTFWCSINTADWVLPGKKMGNLSQ

Parental  LSSGEDKWLLRKKAQEVLLNSPLQEERKFPPDHYGLPAVCDLFACMQLKVDKEKWLYRTPLQV
          LSSGEDK....KKAQ.......L.......P............ACMQLKVDKEKWLY.TPLQ.
Retrocopy LSSGEDKCKIQKKAQKKYYLIHLYRRNISSPQTITVSLQFVISACMQLKVDKEKWLY*TPLQM

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	1.86 RPM	80.45 RPM
SRP051959_heart	1.30 RPM	56.99 RPM
SRP051959_kidney	2.86 RPM	126.77 RPM
SRP051959_liver	2.53 RPM	115.95 RPM
SRP051959_lung	2.16 RPM	60.08 RPM
SRP051959_lymph_node	2.15 RPM	45.25 RPM
SRP051959_skeletal_muscle	1.31 RPM	59.99 RPM
SRP051959_spleen	3.38 RPM	86.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_916 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_916 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_916 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019565	1 retrocopy	retro_btau_1761,
Choloepus hoffmanni	ENSCHOG00000004343	1 retrocopy	retro_chof_2540,
Callithrix jacchus	ENSCJAG00000013352	1 retrocopy	retro_cjac_916 ,
Myotis lucifugus	ENSMLUG00000000619	1 retrocopy	retro_mluc_2161,
Mus musculus	ENSMUSG00000056234	1 retrocopy	retro_mmus_14,