RetrogeneDB ID: retro_cjac_4224

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:138222350..138223673(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAB1
• Ensembl ID: ENSCJAG00000005748
• Aliases: None
• Description: None

Sequence

>retro_cjac_4224
GATGTCCAGCAACTCTATGAAGCAGGAGAATAGGAGTTTTTGGAAATCATGGCACTTGTGGGCATGGCTAGCAAGCTCCT
TCATGTTAGAAGGCTGCAGAAGGCTGTGAGAGACTAGGTCACAAACCCTGGGCTTTTCAATCAGCTGCTGACTTCCCTTC
CTGTCAGTAGCATACCCATCTATAAATTACCAGAGGGATCACCGACATGGCTGGGAATATCCTGCAGTAGTTATGAAAGG
AGTATTAATGCCTGGAAACCTCATTTAAAAATCCCAAATGCGCTGCCACCACCTGTGTGCAGAGCTTGGGACAGGGGAAG
TCAGATGTGGTCGGGAGCCTAGCACTGCCGAGTATTGGTGAGTCCAGACTCTGGCAAAGCCACTGTGCCACGGAGAGCGA
GCAAAGCCTCTTCCCAGCAGACCTGGGCTCCCCTGCATCCCCAGAGGAGAGCAGCGAGGCGCTGGATGCTGCTGTTGCGC
TTTCTGTGAAGCAGATGGCCCCTACACTGCCAAAAAGTGACTTGAACGAAGTGAAAGAGCTACTAAAAACCAACAAGAAG
TTGGCCAAAATGATTGGTCACATCTTTGAGATGAACGATGATGATCCACACAAAGAGGATGAAATTCGGAAATACAGTGC
AATATATGGCAGATTTAACTCAAAGAGGAAGGATGGGAAACATCGCATGCTTCATGAGCTCACTGTTAATGAAGCGGCTG
CTCAACTCTGCATGAAGGATAATGCTCTGCTGACAAGAAGAGATGAACATTTTGCCTTGGCTAGGCCGATTTCTTCAGAA
ATTACCTATAAATATACTTACAGAACCACCAAGTCAAAATGTGGAGAAAGAGATGAATTATCCCCCAAGATAATTAAAGT
GGAGTATGGGTTTTCAGATTTCCAGGATTCTGTGCAAACGCTCTTTTAGCAGGCTAGAACTGTGAGTGAAGAACTTGCAG
CTCTAGTTCACACCAACCTGAAAAGCAGATGAAGTTCCTTTGCAACCACACTGACTATGAGAGACTGCAGCATGCAGAGA
GGAGGTTGTATGCAGGGCTTTACAGGCAGAGCTCAAAAGAGCACAGTCCTAATTGCTTGACTTCCGATAACTCAGATAGA
CAAGGAGAAAGACCTTTCAATCTCCGAATTCCTAATATACAGAACAAACAACCCCATCATTTTGTGGTGGATGGGGAGCT
GAGCCGATTTTACCTCAGTGAGGCAAAGTCCTACTCATCAGTCTTGGGATTTTAAAAGACTATCCTCACTCAGTTTTTAC
CTTAGAAAAGAAAATCATCAAAACAGAGCCTGAAGATTCAAGA

Alignment

ORF - retro_cjac_4224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.36 %
• Parental protein coverage: 92.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALRDWVTNPGLFNQPLTSLPVSSIPIYKLPEGSPTW
          DVQQL.EAGE.EFLEIMALVGMASK.LHVRRLQKA.RD.VTNPGLFNQ.LTSLPVSSIPIYKLPEGSPTW
Retrocopy DVQQLYEAGE*EFLEIMALVGMASKLLHVRRLQKAVRD*VTNPGLFNQLLTSLPVSSIPIYKLPEGSPTW

Parental  LGISCSSYERSSNAREPHLKIP-KCAATTCVQSLGQAKSDVVGSLALQSVGDSRLWQGHHATESEHSLSP
          LGISCSSYERS.NA..PHLKIP.KCAATTCVQSLGQ.KSDVVGSLAL.S.G.SRLWQ.H.ATESE.SL.P
Retrocopy LGISCSSYERSINAWKPHLKIP<KCAATTCVQSLGQGKSDVVGSLALPSIGESRLWQSHCATESEQSLFP

Parental  ADLGSPASPKESSEALDAAAALSVAECVERMAPTLPKSDLNEVKELLKTNKKLAKMIGHIFEMNDDDPHK
          ADLGSPASP.ESSEALDAA.ALS....V..MAPTLPKSDLNEVKELLKTNKKLAKMIGHIFEMNDDDPHK
Retrocopy ADLGSPASPEESSEALDAAVALS----VKQMAPTLPKSDLNEVKELLKTNKKLAKMIGHIFEMNDDDPHK

Parental  EEEIRKYSAIYGRFDSKRKDGKHLTLHELTVNEAAAQLCVKDNALLTRRDELFALARQISREVTYKYTYR
          E.EIRKYSAIYGRF.SKRKDGKH..LHELTVNEAAAQLC.KDNALLTRRDE.FALAR.IS.E.TYKYTYR
Retrocopy EDEIRKYSAIYGRFNSKRKDGKHRMLHELTVNEAAAQLCMKDNALLTRRDEHFALARPISSEITYKYTYR

Parental  TTKSKCGERDELSPKRIKVEDGFPDFQDSVQTLFQQARAKSEELTAL-NSQQPEKVMAKQMEFLCNQAGY
          TTKSKCGERDELSPK.IKVE.GF.DFQDSVQTLF.QAR..SEEL.AL..S.QPEK....QM.FLCN...Y
Retrocopy TTKSKCGERDELSPKIIKVEYGFSDFQDSVQTLF*QARTVSEELAAL<SSHQPEK----QMKFLCNHTDY

Parental  ERLQHVERRLSTGLYRQSSEEHSPNGLTSDNSDGQGERPLNLRMPNLQNRQPHHFVVDGELSRLYPSEAK
          ERLQH.ERRL..GLYRQSS.EHSPN.LTSDNSD.QGERP.NLR.PN.QN.QPHHFVVDGELSR.Y.SEAK
Retrocopy ERLQHAERRLYAGLYRQSSKEHSPNCLTSDNSDRQGERPFNLRIPNIQNKQPHHFVVDGELSRFYLSEAK

Parental  SHSSESLG-ILKDYPHSAFTLEKKVIKTEPEDSR
          S.SS..LG.ILKDYPHS.FTLEKK.IKTEPEDSR
Retrocopy SYSS-VLG<ILKDYPHSVFTLEKKIIKTEPEDSR

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	0.00 RPM	21.10 RPM
SRP051959_heart	0.00 RPM	26.43 RPM
SRP051959_kidney	0.07 RPM	48.06 RPM
SRP051959_liver	0.00 RPM	14.84 RPM
SRP051959_lung	0.03 RPM	30.49 RPM
SRP051959_lymph_node	0.00 RPM	24.25 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.84 RPM
SRP051959_spleen	0.02 RPM	26.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4224 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4224 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4224 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010241	1 retrocopy	retro_chof_2490,
Callithrix jacchus	ENSCJAG00000005748	1 retrocopy	retro_cjac_4224 ,
Gorilla gorilla	ENSGGOG00000013842	1 retrocopy	retro_ggor_3068,
Microcebus murinus	ENSMICG00000007306	2 retrocopies	retro_mmur_1155, retro_mmur_1211,
Nomascus leucogenys	ENSNLEG00000006665	1 retrocopy	retro_nleu_2288,
Pongo abelii	ENSPPYG00000013025	1 retrocopy	retro_pabe_3822,
Ictidomys tridecemlineatus	ENSSTOG00000000098	1 retrocopy	retro_itri_1621,
Tupaia belangeri	ENSTBEG00000011954	1 retrocopy	retro_tbel_3626,