RetrogeneDB ID: retro_cjac_2703

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:22467811..22470618(+)
• Located in intron of: ENSCJAG00000015939

Retrocopy information

• Ensembl ID: ENSCJAG00000015975
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAN1
• Ensembl ID: ENSCJAG00000017520
• Aliases: None
• Description: FANCD2/FANCI-associated nuclease 1 [Source:HGNC Symbol;Acc:29170]

Sequence

>retro_cjac_2703
ATGATGTCAGAAGGGAAACCTTCTGACAGAAAAAAGCCTCCTAGAAGCTTATCAATCAGCAAGAATAAGAAAAAAAGCAT
CTAATTCTATTATTTCATGTTTTAACAATGCACCACCTGCCAAACTTGCCTGCCCCGTTTGCAGTAAAATGGTGCCTAGA
TATGACTTAAATCAGCACCTTGATGAAATGTGTGCTGACAATGATGTCGTTCAAGTTGATCCAGGGCAAGTTGGCATAAT
AAATTCTAATGTGTCTACGGTAGATTTAACCAGTGTTGCTTTAGAAGATGTAATGCCAGAGAAGTCACCACCACCAAAGA
CAAATTTAACTGCTGGCCAAAGTGATTCAGCAAAAATGGCCATAAAACAGAAGTCCAGTCCCTACTTTAAAAGTAATGAT
GACTTGGTGTGCAAAAATCAAGATGAACTGAGAAATCATAGTGTGAAAGTCATTTCTTTGGGAAGCCTAGCATCTAAATT
GTCCAGAAAATACATAAGGGCTAAAAAAATCAATAGATAAGGATGAAGAATTTGCCGGTTGTAGTCCACGGAGTTCCAAA
TCCACGGTCATTCAGAGCCTGGTTGATAACTCTTCAGAAATTGAGGACAAGGATCAAATTTTGGAGAATAGTTCTCAAAA
AGAAAACATGTTTATATGTGATTCTCTAAAGGAAGAGTGTATTCCCGAACACATGGTAAGAGGAAATAAAATAATGGAAG
CCAAAAGCCAAAAGGCTACCCAGGAATGTGAGAAATCAGCCCTTACCCCTGGCTTCTCAGATAATGCTCTCATGTTATTT
TCACCAGATTTCACTCTTGGGAATACATTAAAGTCTACTTCAGACGACAGTCTTGTAAAGCAAGAGTGTATCACAGGAGT
GGTTGGACAACGTGAAGCATGTAGTTGTGAAGAAGTAAAAATGACTGTTGCCTCAGAAGCTAAAATACAGCTGTCAGATT
CAGAGGCAAAATCTCAGAGTTCTGCAGATGATGTTTCTGCATGGAGTAACATCCAAGAGGCTCCTCGGCAGGGTGACAGT
GGCTTAAACAGTGATATCTATCACAGCATTCCTTTGGAGCAGGGGTCAAGCTGCGATGGTCCTGATCAAACAACCAGTCA
TCCTTACTACCTTCGGAGTTTCCTTTTGGTGCTGAAAACCATACTTGAGAATGAAGATGATACGATGCTCTTTGATGAGC
AGGAGAAGGGAATTATAACTAAATTTTATCAGTTATCAGCTACTGGTCAGAAGTTATATGTAAGGCTCTTTCAACGTAAA
TTAAGCTGGATTAAGATGACTAAATTAGAATACGAAGAGATTGCCTCAGGCTTGACACCTGTGATTGAAGAATTGAAGCA
TGCAGGCTTTCTACAGACAGAATCTCAGTTGCAAGAACTCTCTGAAGTGCTTGAACTCCTTTCTGCTCCTGAACTAAAAT
TCATGGCCAAGGCCTTCCATTTGGTGAATCCCAATGGACAGAAACAGCAGCTGGTGGACAGCTTTCTCAAATTGGCCAAA
CAACGTTCAGTCTGCACTTGGGGCAAGAATATGCCTGGAATTGGTGCAGTGATTTTAAAAAGAGCTAAAGCCTTGGCTGG
ACAGTCAGTACGAATCTGTAAAGGCCCCAGGGCTGTGTTTTCCTGGATCATGCTGCTGTTTTCATTGACCAACTCGATGG
AAGATGAAGATGCCACTTGTGGAGGTCAGGGACAGCTTTCAACGGTCCTGTTGGTCAACCTCAGCCGAATGGAGTTTCCT
AGATCGGAAAACCCAATCAATTGGAAAACCCAAATCTTCCAAGACAGAGATGATCTTATTAGATACGCAGCAGCTGTGCA
CATGCTGAGTGACATTTCTTCTGCAATGGCCAACAGGAACTGGGAAGAAGCTAAGGAGCTCGCTCAGTGTTTAAAAAGGG
ATTGGAACAGACTGAAAAACCACCCTTCTCTGAGATGGCATGCAGATTTACCACTCTTTCTGTGGTGTTTTACCGTTGGA
TGGATTTATACAAATATTTTGTCTCGGTCTGTGGAAATACTGCAGAGACTTCACATGTATGAGGAAGCCATCGGGGAACT
TGAAAGCCTTTTGTCTCAGAGAATTTATTGTCCTGACAGCAGAGGCTGATGGTGGGATCGACTGGCTCTTAACGTACACC
AGCACTTGAAGCGCCTGGAACTGGCTACCAAGTGTATCACAGAGGGGCTGGCAGATCTGGAAGTCAGTATGGGACACCGC
CTTTCCCTGTATCAGCGAGCTGTGCGCCTGCAAGAGTCTCCGAGCTGTAAAAAGTACAAACATCTCTTGCAGCAGCTCAC
GGAAATGGCTGTCCAAGATGTGAAACACGTGACCATCACAGGCAGGCTGTGCTCGCAGCGTGGGATGGGCAAGTCCATGT
TTATGATGGAGGCCGGGGAGACTGCTGCCCCCACCACAGTCCTATGCTCCATGGAGGAGCTGGCACTGGCCCATTACAAA
TGCAACAGCTTTGACAAGGGGATTCATGGTGAAGGCTCTACCTTCAGCACCCTGTATGGCCTCCTCCTGTGGGACATCAT
CTTCATGGATGGGATTCAGGATGTCTTCAGAAATGCCTGTCAGGCTTTCCCCCTGGACTTGTGCACAGACAGCTTCTTCA
CAAGCAGAGGCCCGGCTCTTGAAGCCAGGCTACAGCTGATTCACGATGCCCCCGTGGAGAGCCTGTGGTCCTGGGTGGCA
GCCACGTGGCAGGACCAGAAAGGCAGAGTGGCTTCCCTTGTTAGCTGGGATTGCTTCACGTCTCTTGAGCAAGCTCAGGA
TCTCCTG

Alignment

ORF - retro_cjac_2703 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.61 %
• Parental protein coverage: 95.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMSEGKPSDRKKPRRSLSISKNKKK-ASNSIISCFNNAPPAKLACPVCRKMVPRYDLNRHLDEMCANNDV
          MMSEGKPSDRKKP.RSLSISKNKKK.ASNSIISCFNNAPPAKLACPVC.KMVPRYDLN.HLDEMCA.NDV
Retrocopy MMSEGKPSDRKKPPRSLSISKNKKK>ASNSIISCFNNAPPAKLACPVCSKMVPRYDLNQHLDEMCADNDV

Parental  VQVDPGQVGIINSNVSTVDVTSAALEDVMPEKSPPPKANLTAGQSDSAKMAVKHKSSPYFKSNDALVCTN
          VQVDPGQVGIINSNVSTVD.TS.ALEDVMPEKSPPPK.NLTAGQSDSAKMA.K.KSSPYFKSND.LVC.N
Retrocopy VQVDPGQVGIINSNVSTVDLTSVALEDVMPEKSPPPKTNLTAGQSDSAKMAIKQKSSPYFKSNDDLVCKN

Parental  QDELRNRSVKVISLGSLASKLSRKYTRAKK-SIDKDEEFAGSSPQSSRSTVIQSLVDNSSEIEDKDQILE
          QDELRN.SVKVISLGSLASKLSRKY.RAKK.SIDKDEEFAG.SP.SS.STVIQSLVDNSSEIEDKDQILE
Retrocopy QDELRNHSVKVISLGSLASKLSRKYIRAKK>SIDKDEEFAGCSPRSSKSTVIQSLVDNSSEIEDKDQILE

Parental  NSSQKENMFLCDSLKEECIPEHMVRGNKIMEAESQKATQECEKSALTPGFSDNALMLFSPDFTLGNTLKS
          NSSQKENMF.CDSLKEECIPEHMVRGNKIMEA.SQKATQECEKSALTPGFSDNALMLFSPDFTLGNTLKS
Retrocopy NSSQKENMFICDSLKEECIPEHMVRGNKIMEAKSQKATQECEKSALTPGFSDNALMLFSPDFTLGNTLKS

Parental  TSDDSLVKQESITGVVGQREACSCEEVKMTVASEAKIQLSDSEAKSQSSADDVSACSNIQEAPRQGDSGL
          TSDDSLVKQE.ITGVVGQREACSCEEVKMTVASEAKIQLSDSEAKSQSSADDVSA.SNIQEAPRQGDSGL
Retrocopy TSDDSLVKQECITGVVGQREACSCEEVKMTVASEAKIQLSDSEAKSQSSADDVSAWSNIQEAPRQGDSGL

Parental  SSDISRSIPLDQGSSCDGPDQTTSHPYYLRSFLVVLKTVLENEDDMMLFDEQEKGIITKFHQLSGTGQKL
          .SDI..SIPL.QGSSCDGPDQTTSHPYYLRSFL.VLKT.LENEDD.MLFDEQEKGIITKF.QLS.TGQKL
Retrocopy NSDIYHSIPLEQGSSCDGPDQTTSHPYYLRSFLLVLKTILENEDDTMLFDEQEKGIITKFYQLSATGQKL

Parental  YVRLFQRKLSWIKMSKLEYKEIASDLTPVIEELQHAGFLQTESQLQELSEVLELLSAPELKSLAKTFHLL
          YVRLFQRKLSWIKM.KLEY.EIAS.LTPVIEEL.HAGFLQTESQLQELSEVLELLSAPELK..AK.FHL.
Retrocopy YVRLFQRKLSWIKMTKLEYEEIASGLTPVIEELKHAGFLQTESQLQELSEVLELLSAPELKFMAKAFHLV

Parental  NPSGQKQQLVDSFLKLAKQRSVCTWGKNTPGIGAVILKRAKALAGQSVRICKGPRAVFSRILLLFSLTDS
          NP.GQKQQLVDSFLKLAKQRSVCTWGKN.PGIGAVILKRAKALAGQSVRICKGPRAVFS.I.LLFSLT.S
Retrocopy NPNGQKQQLVDSFLKLAKQRSVCTWGKNMPGIGAVILKRAKALAGQSVRICKGPRAVFSWIMLLFSLTNS

Parental  TEDEDAACGGQGQLSTVLLVNLGRMEFP--SYTINRKTQIFQDRDDLIRYAAAVHMLSDISSAMANGNWE
          .EDEDA.CGGQGQLSTVLLVNL.RMEFP.....IN.KTQIFQDRDDLIRYAAAVHMLSDISSAMAN.NWE
Retrocopy MEDEDATCGGQGQLSTVLLVNLSRMEFPRSENPINWKTQIFQDRDDLIRYAAAVHMLSDISSAMANRNWE

Parental  EAKELAQCAKRDWDRLKNHPSLRWHAELPVFLRCFTVGWIYTKILCRSVEILQRLHMYEEAVRELESLLS
          EAKELAQC.KRDW.RLKNHPSLRWHA.LP.FL.CFTVGWIYT.IL.RSVEILQRLHMYEEA..ELESLLS
Retrocopy EAKELAQCLKRDWNRLKNHPSLRWHADLPLFLWCFTVGWIYTNILSRSVEILQRLHMYEEAIGELESLLS

Parental  QRIYCPDSRGRWWDRLALNLHQHLKRLEPAIKCITEGLADPEVRTGHRLSLYQRAVRLRESPSCKKYKHL
          QRIYCPDSRG.WWDRLALN.HQHLKRLE.A.KCITEGLAD.EV..GHRLSLYQRAVRL.ESPSCKKYKHL
Retrocopy QRIYCPDSRG*WWDRLALNVHQHLKRLELATKCITEGLADLEVSMGHRLSLYQRAVRLQESPSCKKYKHL

Parental  LQQLPEMAVQDVKHVTITGRLCPQHGMGKSVFVMEAGETADPTTVLCSVEELALAHYRRNGFDQGIHGEG
          LQQL.EMAVQDVKHVTITGRLC.Q.GMGKS.F.MEAGETA.PTTVLCS.EELALAHY..N.FD.GIHGEG
Retrocopy LQQLTEMAVQDVKHVTITGRLCSQRGMGKSMFMMEAGETAAPTTVLCSMEELALAHYKCNSFDKGIHGEG

Parental  STFSTLYGLLLWDIIFMDGIPDVFRNACQAFPLDLCTDSFFTSRGPALEARLQLIHDAPVESLRAWVAAT
          STFSTLYGLLLWDIIFMDGI.DVFRNACQAFPLDLCTDSFFTSRGPALEARLQLIHDAPVESL..WVAAT
Retrocopy STFSTLYGLLLWDIIFMDGIQDVFRNACQAFPLDLCTDSFFTSRGPALEARLQLIHDAPVESLWSWVAAT

Parental  WQDQEGRVASLVSWDRFTSLEQAQDLV
          WQDQ.GRVASLVSWD.FTSLEQAQDL.
Retrocopy WQDQKGRVASLVSWDCFTSLEQAQDLL

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	1.40 RPM	18.77 RPM
SRP051959_heart	3.30 RPM	21.26 RPM
SRP051959_kidney	1.80 RPM	31.84 RPM
SRP051959_liver	3.10 RPM	19.08 RPM
SRP051959_lung	2.41 RPM	28.13 RPM
SRP051959_lymph_node	1.35 RPM	33.99 RPM
SRP051959_skeletal_muscle	2.42 RPM	19.65 RPM
SRP051959_spleen	1.26 RPM	29.60 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2703 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2703 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2703 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017520	1 retrocopy	retro_cjac_2703 ,