RetrogeneDB ID: retro_cjac_2537

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:80695954..80697171(+)
• Located in intron of: ENSCJAG00000037483

Retrocopy information

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

Parental gene information

• Parental gene symbol: UAP1
• Ensembl ID: ENSCJAG00000004264
• Aliases: None
• Description: None

Sequence

>retro_cjac_2537
ATGAACATTAATGACCCCGAACTCAGGTTGTCCCAAGCTGAGCAAGAACATCCACTCCGTTTTTGGAATGAGCTTAAAGA
AGCTCAACAGGAAGAACTTTATGCAAAGCTCCAGGCCATGAACTTTGAGGAGCTGGACTTCTTTTTCCAAAAGGCCATTG
AAGGATTTAACCAGTCCTCTAAGCAAGAAAAAATGGATGCGTGAATGGAACCTGTCCCTTGAGAGATATTGGGTAGTGCT
ACAGGGAATCTAGATCAGCTCCAGGCCTGGGAAAGTGAAGAACTTTTCCAGATTTCTCAGAACGAAGTAACACTTCTAGT
TGGTGGGCAGGGGACTAGACTCATTGCATATCCAAAGGGGATGTATGATGTTAGTTTGCCATCCCAAAAGAGGCTTTTTC
AGTTTCAAGTAGAGTGTATCCTGAAGCTACAACAGCTGAAAAATATTATGGCATCAAATGCATTATTTCTTATAATAATC
AGTAGCAGAACAGTGGAATCTACAAAGGAGTTCTTCACCAATCACAGGTACTTTGGTTTGAAAAAAGAAGATAAAATCTT
TTTTCAGCAAGGAATGCTCCCTGCCATGAGTTTTGATGAGCAAATTATTTTGGAAGAGAAGAACAAAGTTTCTATGGCTC
CAGATAAGATAGTGGTCTTTATCGGGCTTTTGCAGCCTGGAATACTGTGGAGGAGATGGAGCAAAGAGGCATCTGGAACA
TTCATGTGTATTGTGTTGACAACATATTAGTAAAAGTGGCAGACCCACGGTTCATTGGATTTTGCATTCCAAAAGGAGCA
GACTGTGGAGCAAAGGTGGTAGAGAAAACAAACCCTACAGAATGGGTTGGAATAGTTTGCCAAGTGAATGGAGTTTACCA
GGTGGTAGAATATAGTGATATTTCCCTGGCAACAGTTCAAAAACGAAGCTCAGATGAATGACTGCTGTTTCATGTGGGGA
ACATGGCCAGCCATTTCCTCACTGTACCACTTCTGAGAGATGTTGTCAATGTTTATGAACTTCATTTGCAGCACCATGTG
GCTCAAAAGAAGATTCCTTATGTGGATACCCATTAGCAATTAATTAAACCAGATAAACCTAGTGGAATAAGTGTAGGAAA
ATTTGTCTTTGACATCTCCTAGTTTACAAAGAAGTTTGTGGTATATGAAATATTACAGGAAGATGACTTTTCCACACTAA
AGAATGCTGACAGACAA

Alignment

ORF - retro_cjac_2537 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.54 %
• Parental protein coverage: 81.58 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNIDDLQLRLSKAGQEHLLRFWNELEEAQQVELHAELQAMNFEELNLFFQKAIEGFNQSSQQKNVDARME
          MNI.D..LRLS.A.QEH.LRFWNEL.EAQQ.EL.A.LQAMNFEEL..FFQKAIEGFNQSS.Q...DA.ME
Retrocopy MNINDPELRLSQAEQEHPLRFWNELKEAQQEELYAKLQAMNFEELDFFFQKAIEGFNQSSKQEKMDA*ME

Parental  PVPREVLGSATRDQDQLQAWESEGLSQISQNKVAVLLLAGGQGTRLGVAYPKGMYDVGLPSHKTLFQIQA
          PVP.E.LGSAT...DQLQAWESE.L.QISQN.V...LL.GGQGTRL..AYPKGMYDV.LPS.K.LFQ.Q.
Retrocopy PVP*EILGSATGNLDQLQAWESEELFQISQNEVT--LLVGGQGTRL-IAYPKGMYDVSLPSQKRLFQFQV

Parental  ERILKLQQVAEKYYGNKCIIPWYIMTSGRTMESTKEFFTKHKYFGLKKENVIFFQQGMLPAMSFDGKIIL
          E.ILKLQQ.......N.......I..S.RT.ESTKEFFT.H.YFGLKKE..IFFQQGMLPAMSFD..IIL
Retrocopy ECILKLQQLKNIMASNALFL---IIISSRTVESTKEFFTNHRYFGLKKEDKIFFQQGMLPAMSFDEQIIL

Parental  EEKNKVSMAPDG-NGGLYRALAAQNIVEDMEQRGIWSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKV
          EEKNKVSMAPD....GLYRA.AA.N.VE.MEQRGIW.IHVYCVDNILVKVADPRFIGFCI.KGADCGAKV
Retrocopy EEKNKVSMAPDK<DSGLYRAFAAWNTVEEMEQRGIWNIHVYCVDNILVKVADPRFIGFCIPKGADCGAKV

Parental  VEKTNPTEPVGVVCRVDGVYQVVEYSEISLATAQKRSSDGRLLFNAGNIANHFFTVPFLRDVVNVYEPQL
          VEKTNPTE.VG.VC.V.GVYQVVEYS.ISLAT.QKRSSD..LLF..GN.A.HF.TVP.LRDVVNVYE..L
Retrocopy VEKTNPTEWVGIVCQVNGVYQVVEYSDISLATVQKRSSDE*LLFHVGNMASHFLTVPLLRDVVNVYELHL

Parental  QHHVAQKKIPYVDTRGQLIKPDKPNGIKMEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQ
          QHHVAQKKIPYVDT..QLIKPDKP.GI...KFVFDI..F.KKFVVYE.L.ED.FS.LKNAD.Q
Retrocopy QHHVAQKKIPYVDTH*QLIKPDKPSGISVGKFVFDIS*FTKKFVVYEILQEDDFSTLKNADRQ

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	0.04 RPM	80.21 RPM
SRP051959_heart	0.11 RPM	35.92 RPM
SRP051959_kidney	0.02 RPM	24.18 RPM
SRP051959_liver	0.02 RPM	38.69 RPM
SRP051959_lung	0.11 RPM	23.12 RPM
SRP051959_lymph_node	0.02 RPM	20.68 RPM
SRP051959_skeletal_muscle	0.04 RPM	13.56 RPM
SRP051959_spleen	0.02 RPM	23.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2537 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2537 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2537 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004264	1 retrocopy	retro_cjac_2537 ,
Cavia porcellus	ENSCPOG00000004568	5 retrocopies	retro_cpor_1186, retro_cpor_1187, retro_cpor_1188, retro_cpor_1189, retro_cpor_511,
Dasypus novemcinctus	ENSDNOG00000024661	1 retrocopy	retro_dnov_1035,
Macaca mulatta	ENSMMUG00000019514	1 retrocopy	retro_mmul_1238,
Tarsius syrichta	ENSTSYG00000002725	3 retrocopies	retro_tsyr_121, retro_tsyr_390, retro_tsyr_582,