RetrogeneDB ID: retro_cjac_2137

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:50005499..50006594(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFSD10
• Ensembl ID: ENSCJAG00000014217
• Aliases: None
• Description: major facilitator superfamily domain containing 10 [Source:HGNC Symbol;Acc:16894]

Sequence

>retro_cjac_2137
GGTCTGATTGGCTTGGCCTCTGTTCTACAGCTTCTTGCTGTGTCACTCACTGGGGCCAGCTCTGACTGCTTGGAGAGGTG
CCCCTTGATGCTGCTGTCCCTGACGGGTGTGGCCACCTCATATGCCATCTGGGCCACCTCTAGGAGCTTTGCGGCCTTCC
TGGCCTCCAGGCTGATTGGGGGCATCAGCAAGGGGAACGTCAGCCTCTCCACGGCCATCATTGCTGACCTGGGCTCGCCT
CTGGCCTGCAGCCAAGGCATGGCGGTCAGCGGGGTGGCCTTCTCCCTGGACTTCACCCTGGGCCCTATGCTTGCAGGCTC
GCTGCCCATAGAAATGGCACCCTGGTTTGCCCTTTTCTTCGCAGCCTCTGATCTGCTGTTCATCTCCTGCTTCCTGCCAG
AGATGCTGCCCCTGGAGAAACCGGGCGCCCTCTGTCGCTCTAGGGTTCCGCGGTGCAGCGGATCTGCTCAGCCTCCTGGC
CCTGTTGCGCTTCTCCGCTGTGGCTTGTGGCCAGGACCCACCCGCTGGAGGCAGGCTTAGCAGCCTGCGCCGCCTGGGCC
TAGTCGGCTTCCTCTACCTCTTCCTGTTCTCAGGCCGGGAGTACACGCTGAGCTTCCTAGCACAACAGCGCTTCCAGTTC
AGCAGCCTGCAGCAGGGGAAGATATTATTTCCTTATCTGCTTCACCATGACCACCATCCAGGGTGCCTGTGCCTGGCGGA
TCCATCCTGGCAGGAAAGTCTCTGCCATGATGCGGGCCCTCCTGCTGCTGGTGCCTGCCTTCCTCCTCATCGGCTGGGAC
CATTCTCTGCCAATGCTAGGCATTGGCTGCTGCTCTACTCCATTGCCTCTGCTGTTGTGGTGCCCTGCCTGTCCTCCGTG
GTAGCTGGCTAAGGCTCGCCAGAGCAGAAGGGCACGGTCATGGGCACACTGCCTAGCCTAGGCACTCTGGCCAGGGCCGC
GGGGCCCCTGGTGGCGGCTTCAGTGTACTGGCTGCCCAGAGCCCAGGCCTGCTTCACTGCGTGGTACTAGCTCTTCCTGC
TCCCCTTCCTTGTCCTGCGAAGCTGAGTTGTCCAGCGCAGACGCTCAAGGCCGAG

Alignment

ORF - retro_cjac_2137 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GLIGSAFSVLQFLSAPLTGATSDCLGRRPMMLLSLTGVATSYAVWATSGSFAAFLASRLIGGISKGNVSL
          GLIG.A.SVLQ.L...LTGA.SDCL.R.P.MLLSLTGVATSYA.WATS.SFAAFLASRLIGGISKGNVSL
Retrocopy GLIGLA-SVLQLLAVSLTGASSDCLERCPLMLLSLTGVATSYAIWATSRSFAAFLASRLIGGISKGNVSL

Parental  STAIIADLSSPLARSQGMAVIGVAFSLGFTLGPMLGASLPVEMAPWFALLFTASDLLFIFCFLPETLPVE
          STAIIADL.SPLA.SQGMAV.GVAFSL.FTLGPML..SLP.EMAPWFAL.F.ASDLLFI.CFLPE.LP.E
Retrocopy STAIIADLGSPLACSQGMAVSGVAFSLDFTLGPMLAGSLPIEMAPWFALFFAASDLLFISCFLPEMLPLE

Parental  K-RAPSIALGFRGAADLLSPLALLHFSAVAHGQNPPAGDRLSSLRRLGLVYFIYLFLFSGLEYTLSFLTH
          K.RAPS.ALGFRGAADLLS.LALL.FSAVA.GQ.PPAG.RLSSLRRLGLV.F.YLFLFSG.EYTLSFL..
Retrocopy K>RAPSVALGFRGAADLLSLLALLRFSAVACGQDPPAGGRLSSLRRLGLVGFLYLFLFSGREYTLSFLAQ

Parental  QRFQFSSLQQGKM-FFLIGLTMATIQGAYARRIHPGGEVAAVKRALLLLVPAFLLIGWGHSLPMLGLG-L
          QRFQFSSLQQGK...FLI..TM.TIQGA.A.RIHPG..V.A..RALLLLVPAFLLIGW.HSLPMLG.G.L
Retrocopy QRFQFSSLQQGKI>YFLICFTMTTIQGACAWRIHPGRKVSAMMRALLLLVPAFLLIGWDHSLPMLGIG<L

Parental  LLYSFAAAVVVPCLSSVVAGYGSPGQKGTVMGTLRSLGALARAAGPLVAASVYWLAGAQACFTVWSGLFL
          LLYS.A.AVVVPCLSSVVAG.GSP.QKGTVMGTL.SLG.LARAAGPLVAASVYWL..AQACFT.W..LFL
Retrocopy LLYSIASAVVVPCLSSVVAG*GSPEQKGTVMGTLPSLGTLARAAGPLVAASVYWLPRAQACFTAWY*LFL

Parental  LPFLLLR-KLSCPAQMLKAE
          LPFL.LR.KLSCPAQ.LKAE
Retrocopy LPFLVLR<KLSCPAQTLKAE

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	0.07 RPM	3.13 RPM
SRP051959_heart	0.26 RPM	7.58 RPM
SRP051959_kidney	0.00 RPM	8.96 RPM
SRP051959_liver	0.00 RPM	3.27 RPM
SRP051959_lung	0.02 RPM	9.09 RPM
SRP051959_lymph_node	0.02 RPM	9.82 RPM
SRP051959_skeletal_muscle	0.28 RPM	5.13 RPM
SRP051959_spleen	0.04 RPM	7.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2137 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2137 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2137 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	ENSCJAG00000014217	1 retrocopy	retro_cjac_2137 ,