RetrogeneDB ID: retro_cjac_2135

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:47635942..47636799(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1M1
• Ensembl ID: ENSCJAG00000014070
• Aliases: None
• Description: None

Sequence

>retro_cjac_2135
CAGCAGAGCAACAAGCTGAGACAGGCAAATCACGAGTGCACCCACTGTCACCAATGCTGTGTCCTGGCGCTCTAAGGGTA
TCAAGTATAAGAAGAACGAGGTCTTCATCGATGTCATAGAGTCTGTCAACCTGCTGGTCAATGCCAACGGCAGCGTCCTG
CTGAGCGAGATCGTTGGTAGCATCAAGCTCAAGGTGTTTCTGTCGGGAATGCCTGAGCTGCGGCTGGGCCTCAATGACCG
CGTGCTCTTTGAGCTCACTGGCCTTTCAGGCAGCAAGAACAAATCGGTGGAGCTGGAGGATGTGAAATTCCACCAGTGTG
TGCGGCTCTCACGCTTTGACAACGACCGCACCATCTCCTTCATCCCGCCTGATGGTGACTTTGAGCTCATGTCCTACCGC
CTCAGCACCCAGGTGAAGCCACTGATCTGGATTGAGTCTGTCATTGAGAAGTTCTCCCACAGCCGTGTGGAGATCATGGT
CAAGGCCAAGGGGCAGTTTAAGAAACAGTCAGTGGCCAACGGTGTGGAGATATCTGTGCCTGTGCCTAGTGATGCCGACT
CCCCCAGATTCAAGACCAGTGTGGGCAGCGCCAAGTATGTGCCAGAGAAAAACGTCGTGGAGTATTAAGTCTTTCCCGGG
GGGCAAGGAGTACTTGATGCGAGCCCACTTTGGCCTCCCCAGTGTGGAGAAGGAGGAGGTGGAGGGCCGGCCCCCTATCG
GGGTCAAGTTTGAGATCCCCTGCTTCACCGTCTCTGGGATCCAGGTCAGATACATGAAGATAATTGAGAAAAGCGGTTAC
CAGGCCCTGCCCTGGGTTCGCTACATCACCCAGAGTGGCGATTACCAGCTTCGTACC

Alignment

ORF - retro_cjac_2135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.63 %
• Parental protein coverage: 81.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QEGHKL-ETGAPR-PPATVTNAVSWRSEGIKYRKNEVFLDVIESVNLLVSANGNAC-SEIVGSIKMRVFL
          Q...KL.ETG..R....TVTNAVSWRS.GIKY.KNEVF.DVIESVNLLV.ANG....SEIVGSIK..VFL
Retrocopy QQSNKL<ETGKSR<SAPTVTNAVSWRSKGIKYKKNEVFIDVIESVNLLVNANGSVLLSEIVGSIKLKVFL

Parental  SGMPELRLGLNDKVLFDNTGRG--KSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTH
          SGMPELRLGLND.VLF..TG....K.KSVELEDVKFHQCVRLSRF.NDRTISFIPPDG.FELMSYRL.T.
Retrocopy SGMPELRLGLNDRVLFELTGLSGSKNKSVELEDVKFHQCVRLSRFDNDRTISFIPPDGDFELMSYRLSTQ

Parental  VKPLIWIESVIEKHSHSRIEYMIKAKSQFKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIV
          VKPLIWIESVIEK.SHSR.E.M.KAK.QFK..S.AN.VEI..PVP.DADSP.FKT.VGS.K.VPE.....
Retrocopy VKPLIWIESVIEKFSHSRVEIMVKAKGQFKKQSVANGVEISVPVPSDADSPRFKTSVGSAKYVPEKNVVE

Parental  WSIKSFP-GGKEYLMRAHFGLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRY
          .....FP.GGKEYLMRAHFGLPSVE.E..EG.PPI.VKFEIP.FT.SGIQVRY.KIIEKSGYQALPWVRY
Retrocopy Y*V--FP>GGKEYLMRAHFGLPSVEKEEVEGRPPIGVKFEIPCFTVSGIQVRYMKIIEKSGYQALPWVRY

Parental  ITQNGDYQLRT
          ITQ.GDYQLRT
Retrocopy ITQSGDYQLRT

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	0.62 RPM	6.66 RPM
SRP051959_heart	0.00 RPM	10.80 RPM
SRP051959_kidney	0.29 RPM	13.67 RPM
SRP051959_liver	0.02 RPM	14.95 RPM
SRP051959_lung	0.08 RPM	10.87 RPM
SRP051959_lymph_node	0.00 RPM	13.95 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.58 RPM
SRP051959_spleen	0.00 RPM	12.98 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2135 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2135 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2135 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012998	1 retrocopy	retro_cjac_3340,
Callithrix jacchus	ENSCJAG00000014070	3 retrocopies	retro_cjac_1985, retro_cjac_2135 , retro_cjac_3873,