RetrogeneDB ID: retro_cjac_1985

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 20:4538523..4539792(+)
• 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_1985
ATGTCCACCTCAGCTGTCTTCATTCTCGATGTCAAGGGCAAGCCCCTGATCAGCCACAACTGCAAGGGCAATGTGCCCAT
GAGCAAGATTGATTACTTCATGCCTCTGCTGGTGCAGCAGGATGAGGAGGGCTCCCTCACCCTAAGGCTGAGCTATGGCA
AGGTCCACTTCCTATGGATCAAACACAGCAACCTCTACCTGGTGGCCACCACATTGAAGAATGCCAATGCCTCACTGGTG
TGCTCTTTCCTGTATAAGACAATAGAGGAATTCTGTGAATACTTCAAGGAGCTGTAGGAGAGCATCAGGGACAACTTTGT
CATCGTCTATGAGTTGCTGGACAAGCTCATGGACTTTGGCTTCCCGCAGACCACCGACATCAAGATCCTGCAGGAGTACA
TCACTCAGCAGAGCAACAAGCTGGAGATGGGTTAATCATGGGTACCACCCACTGTCACCAATGCTGTGTCCTGGCACTCT
GAGGCTATCAAGTATAAGAAGAACGAGGTCTTCATCGATGTCATAGAGTCTGTCAACCTGCTGGTCAATGCCAATGACAG
TGTCCTGCTGAGCGAGATCATTGGTACCATCAACCTCAAAGTGCTTCTGTCAGGAATGCCTGAGCTGCGGCTGGGCCTCA
ATGACCATGTGCTCTTTGAGCTCACTGGCTACAGCAAGAACAAATTGTTAGAGCTAGAGGATATGAAATTCCACCAGTGT
GTGCAGCTCTCATGCTTTGACAACAACCGCACCATCTCTTTCATCCTGCCTGATGATGACTTTGAGCTCATGTCCTACCG
CCTCAGCACCCAGGTGAAGCCACTGATCTGGATTGAGTTTGTCATTGGGAAGTTCTCCCACAGCCATGTGGAGATCTTAG
TCAAGACCAAGGGGCAGTTTAAGAAACAGTCAGTGGCCAATGGTGTGGAGATATCTGTGCCTGTGCCTGTGCCCAGTGAT
GCCGACTCCCCCAGATTCAAGACCAGTGTGGGCAGTGCTAACTATGTGCCAGAGAAAAACATTGTGATTTAGAGTATTAA
GTCTTTCCTGGGGAGCAAGGAGTGCTTGATGCGAGCCCACTTTGGCCTCCCCAGCATGGAGAAGGAGGAGGTGGAGGGCC
GGCCCCCTATCCGGGTCAAGTTTGAGATCCTCTACTTCACCATCTCTGGGATCCAGGTCCGATACATGAAGATCATTGAG
AAAAGTGGTCACCAGGCCCTGCCCTGGGTTCACTACATCACCCAGAGTGGCAATTACCAACTTCATACC

Alignment

ORF - retro_cjac_1985 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.92 %
• Parental protein coverage: 99.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWIKHNNLYLVAT
          MS.SAV..LD.KGK.LI..N..G.V.MS....FMP.L....EEG.L...L..G.V.F.WIKH.NLYLVAT
Retrocopy MSTSAVFILDVKGKPLISHNCKGNVPMSKIDYFMPLLVQQDEEGSLTLRLSYGKVHFLWIKHSNLYLVAT

Parental  SKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDFGYPQTTDSKILQEYITQEGH
          ..KNA..SLV.SFLYK....F.EYFKEL.E.SIRDNFVI.YELLD.LMDFG.PQTTD.KILQEYITQ...
Retrocopy TLKNANASLVCSFLYKTIEEFCEYFKEL*E-SIRDNFVIVYELLDKLMDFGFPQTTDIKILQEYITQQSN

Parental  KLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIESVNLLVSANGNAC-SEIVGSIKMRVFLSGMPEL
          KLE.G....P.TVTNAVSW.SE.IKY.KNEVF.DVIESVNLLV.AN.....SEI.G.I...V.LSGMPEL
Retrocopy KLEMG*SWVPPTVTNAVSWHSEAIKYKKNEVFIDVIESVNLLVNANDSVLLSEIIGTINLKVLLSGMPEL

Parental  RLGLNDKVLFDNTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIE
          RLGLND.VLF..TG..K.K..ELED.KFHQCV.LS.F.N.RTISFI.PD..FELMSYRL.T.VKPLIWIE
Retrocopy RLGLNDHVLFELTGYSKNKLLELEDMKFHQCVQLSCFDNNRTISFILPDDDFELMSYRLSTQVKPLIWIE

Parental  SVIEKHSHSRIEYMIKAKSQFKRRSTANNVEIH--IPVPNDADSPKFKTTVGSVKWVPENSEIVWSIKSF
          .VI.K.SHS..E...K.K.QFK..S.AN.VEI....PVP.DADSP.FKT.VGS...VPE......SIKSF
Retrocopy FVIGKFSHSHVEILVKTKGQFKKQSVANGVEISVPVPVPSDADSPRFKTSVGSANYVPEKNIVI*SIKSF

Parental  PGGKEYLMRAHFGLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDY
          .G.KE.LMRAHFGLPS.E.E..EG.PPI.VKFEI.YFT.SGIQVRY.KIIEKSG.QALPWV.YITQ.G.Y
Retrocopy LGSKECLMRAHFGLPSMEKEEVEGRPPIRVKFEILYFTISGIQVRYMKIIEKSGHQALPWVHYITQSGNY

Parental  QLRT
          QL.T
Retrocopy QLHT

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	6.66 RPM
SRP051959_heart	0.00 RPM	10.80 RPM
SRP051959_kidney	0.00 RPM	13.67 RPM
SRP051959_liver	0.00 RPM	14.95 RPM
SRP051959_lung	0.00 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_1985 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1985 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1985 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,