RetrogeneDB ID: retro_cjac_1396

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:45744927..45745838(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM43
• Ensembl ID: ENSCJAG00000003125
• Aliases: None
• Description: RNA binding motif protein 43 [Source:HGNC Symbol;Acc:24790]

Sequence

>retro_cjac_1396
AGGGCATCACTTTTGAATGCCAAGGAATCCAAAGCTTTGAAGGAACAGTTGTAGTTGCTGGTCTTCTGGGTGGCCTTTTT
AGTGAAGAGGCCATATTATTGGTCACATTAGTGAAGAGGCACTTCCAAGATATTAAGAATGAGGGTGGAGATGTTGGAGA
TGTGATATATCCAACAGAAACCAAGGGAGTTGCATATGTAATATGCAAAGAAAGAAAAAGTTGCAGAGAATGTCATCAGA
CAAAAGAAACACCAGCTAGCAAGGAAGGCCTGACACGCTGAACTCATAGTCTCTCATTTTAGTAACAGGGTCTTCAGTTC
TGTAAATCCTATCCTTGATCGTTCTGTTTTTGGGAGTGAAGTTACTCTAGAAATTCTGGTGATGAACCTGAAAAAGAAAA
TCCCAACTTTAAGCTTCAGTCCTTTGGAAGCTAGTGGAAGACTCCATGGAAGGATCATTTCTTGCTGTCAGAGAGGCTCA
ACGAATCTTTGTGAGTAAAAGCAAGTTCTCTTTTAGAAAAAAAAAAGAGAAATTTTACCAGTGAGGAGAGAAAGTAGAAT
AAATAGAGCCCCCAAAGGAATCTATAAAGAAGCAGTGACTCTTTGGAGTCAGTCAGGACCTTAGTACCTGAGACTGCTAG
AAGTGGAGAAACACCTGTTCTCAACACAGATGTTTTACTTTATCTGAAACAGAAATGTGGATGTTTTGAAAGCACACTGA
ACAAATTCCATATTCTGCCTCAGAAGAGAGTGGATGGTGAAATCACCACAATTTGCCTAAAAAGTACTCAAGCTGGTTCT
CAGCCAAACCACCCAAAACATGTAAAGGAGTTCATTGAGGAATGGTCACATGCTCTTCACTTAGAGCTTAGAAAAGAGGC
ATTTATTTTGGAAACAAAAGGCAGGGGGGAG

Alignment

ORF - retro_cjac_1396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.38 %
• Parental protein coverage: 85.27 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QASVLNVKESK-DSERTVVVAGLPVGLFIDQ--LLVILVKKHFQDIKNEGGDVEDVIYPTRTKGVAYVIF
          .AS.LN.KESK...E.TVVVAGL..GLF.....LLV.LVK.HFQDIKNEGGDV.DVIYPT.TKGVAYVI.
Retrocopy RASLLNAKESK<SFEGTVVVAGLLGGLFSEEAILLVTLVKRHFQDIKNEGGDVGDVIYPTETKGVAYVIC

Parental  KEKK-VAENVIRQKKHWLARKAGHTELTVSHFSDKIFSSVNAILDLSVFGNEVTLETLVKDLKKKIPTLS
          KE.K.VAENVIRQKKH.LARKA.H.EL.VSHFS...FSSVN.ILD.SVFG.EVTLE.LV..LKKKIPTLS
Retrocopy KERK>VAENVIRQKKHQLARKA*HAELIVSHFSNRVFSSVNPILDRSVFGSEVTLEILVMNLKKKIPTLS

Parental  FSPLKPNGRI-TVEGSFLAVKRLKESLLVRASSFLE-KNRNFTSEGRKWNRRNPQKNLQRSNNYLVSVRT
          FSPL...GR.......FL...RL.ESL.V.ASS.LE.K.RNFTSE.RK.N...PQ.NL.RS...L.SVRT
Retrocopy FSPLEASGRL<PWKDHFLLSERLNESL*VKASSLLEKKKRNFTSEERK*NK*SPQRNL*RSSDSLESVRT

Parental  LVPETARNGEMLVLDTDIFLYLKHRCEFYESTLKKFHILSEEKIDGEITTIYLKNFQVGSQPNNAKHVKE
          LVPETAR.GE..VL.TD..LYLK..C...ESTL.KFHIL.....DGEITTI.LK..Q.GSQPN..KHVKE
Retrocopy LVPETARSGETPVLNTDVLLYLKQKCGCFESTLNKFHILPQKRVDGEITTICLKSTQAGSQPNHPKHVKE

Parental  LIEEWSHALHLELRKETFILKGKENRE
          .IEEWSHALHLELRKE.FIL..K...E
Retrocopy FIEEWSHALHLELRKEAFILETKGRGE

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	6.55 RPM
SRP051959_heart	1.42 RPM	5.68 RPM
SRP051959_kidney	0.13 RPM	6.74 RPM
SRP051959_liver	0.06 RPM	7.73 RPM
SRP051959_lung	0.31 RPM	9.86 RPM
SRP051959_lymph_node	0.00 RPM	9.27 RPM
SRP051959_skeletal_muscle	0.09 RPM	1.22 RPM
SRP051959_spleen	0.69 RPM	14.12 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1396 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1396 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1396 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003125	1 retrocopy	retro_cjac_1396 ,
Nomascus leucogenys	ENSNLEG00000010889	1 retrocopy	retro_nleu_1537,