RetrogeneDB ID: retro_cjac_1094

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:39958135..39958976(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNIP1
• Ensembl ID: ENSCJAG00000001963
• Aliases: None
• Description: Smad nuclear interacting protein 1 [Source:HGNC Symbol;Acc:30587]

Sequence

>retro_cjac_1094
CCAGACACTGTCTACTATCAGGGAGTTCGTGTTTAGTGAGAGAGCCCAGAAGCGGCCCATCCTGCCCACCATCGGCCAGA
CCGCTCAGCAGTAGCCAGCAAGCTGAGCCGCCCGGGCCACCGTGGGAACCAAGCCCGAGGATTTAGCCGGTCCCAACAAA
AAAAGAAAAACAAGTCCCCAGGGAGAAGAAGCAAGTCTGCTCGGATTAAGAGGACCCGAAGTCCTCACCACTAACAGTCA
AAGTGAAGCAGGAGCCTGAGGATCATCCCCAGGGAGGACGGGAGGATCGGCAGCACAGGGAACCGTGAAAACAGGAACAC
AGGAGAGCTAGGAACAGTGACCGGGACAGACACCGGGGCCATTCCCTCTGAAGGAAAACGTCTAACGGGAGGCCTGGGAG
TAGGCAGGGTCAGGGACGGGATCCAGACACTCAGAACCTGCAGGCTCAGGAAGACCAGCTGGAGTTTCACAATGCCAGGC
GGGGGGCATCGCCAGAAGAATGACGCTGGTGGCGGTGGCAGTGAGTCTCACGAGTTGTTTCCTCGGCCTGGTGGCAACAA
AAAAAAAAAAAGGTGACTGTTAAAGAAAAACCAAGCTTTGAACTTTCTGGGGCGCTTCTTGAGGACACCAACACTTTTCT
GGGTGCAGTAATTAAATACACTGAGCCCCCAGAAGCACATACTCCCAGAAAACTGTGGCATCTCTACCCGTTTAAAAATG
ATGAGGTGCTGCCAGTCATGTACATACACCAAGACAAGAGTGCATACCTACTGGGTGACACCGCCGCATTGCAGACATTG
CAATCGATCGCCCATCTTGTTCAAAGGAGCATGTGGTCTGG

Alignment

ORF - retro_cjac_1094 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.44 %
• Parental protein coverage: 71.46 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PATVVVKQERLSPEAAPPAHRRPDHSGGSPSPPASEPSRPGHRGNRARGVSRSPPKKKNKSSGRRSKSPR
          P.TV.....R...E....AH..P.H.....S..AS..SRPGHRGN.ARG.SRS..KKKNKS.GRRSKS.R
Retrocopy PDTVYYQGVRV**ESPEAAH--PAHHRPDRSAVASKLSRPGHRGNQARGFSRSQQKKKNKSPGRRSKSAR

Parental  SKRTRSPHH-STVKVKQEREDHPRRGREDRQHREPSEQEHRRARNSDRDRHRGHSHQRRTSDERPGSGQG
          .KRTRSPHH..TVKVKQE.EDHP..GREDRQHREP..QEHRRARNSDRDRHRGHS..R.TS..RPGS.QG
Retrocopy IKRTRSPHH<LTVKVKQEPEDHPQGGREDRQHREP*KQEHRRARNSDRDRHRGHSL*RKTSNGRPGSRQG

Parental  QGRDRDTQNLQAQEDERVFYNARR-REHRQRNDVGGGGSETQELVPQPGGN-NKEKEVPVKEKPSFELSG
          QGRD.DTQNLQAQED...F.NARR..........GG.GSE..EL.P.PGGN..K.K.V.VKEKPSFELSG
Retrocopy QGRDPDTQNLQAQEDQLEFHNARR>GHRQKNDAGGG-GSESHELFPRPGGN<QKKKKVTVKEKPSFELSG

Parental  ALLEDTNTFRGVVIKYSEPPEARIPKKRWRLYPFKNDEVLPVMYIHR-QSAYLLGR-HRRIADIPIDHPS
          ALLEDTNTF.G.VIKY.EPPEA..P.K.W.LYPFKNDEVLPVMYIH...SAYLLG..HRRIADI.ID.PS
Retrocopy ALLEDTNTFLGAVIKYTEPPEAHTPRKLWHLYPFKNDEVLPVMYIHQDKSAYLLGD<HRRIADIAIDRPS

Parental  CSKQHAVF
          CSK.H.V.
Retrocopy CSKEHVVW

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	3.24 RPM	8.34 RPM
SRP051959_heart	7.49 RPM	6.30 RPM
SRP051959_kidney	5.81 RPM	6.28 RPM
SRP051959_liver	3.47 RPM	5.09 RPM
SRP051959_lung	7.16 RPM	10.53 RPM
SRP051959_lymph_node	7.72 RPM	12.63 RPM
SRP051959_skeletal_muscle	14.72 RPM	5.98 RPM
SRP051959_spleen	5.06 RPM	9.31 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_cjac_1094 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
HX490195	39958148	39958446	100	298	0	298
HX604429	39958148	39958465	99.7	316	1	315

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1094 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1094 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001963	1 retrocopy	retro_cjac_1094 ,
Myotis lucifugus	ENSMLUG00000017132	2 retrocopies	retro_mluc_1400, retro_mluc_159,
Mus musculus	ENSMUSG00000050213	2 retrocopies	retro_mmus_3038, retro_mmus_941,
Otolemur garnettii	ENSOGAG00000008634	2 retrocopies	retro_ogar_2306, retro_ogar_893,