RetrogeneDB ID: retro_cjac_3596

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01187211.1:5458..6615(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000033945
• Aliases: None
• Description: None

Sequence

>retro_cjac_3596
GAAAAGCCCAAGACTGAAGATGTGGGTTCAGATGAGGAGGATGATAGTGGTAAGGATAAGAAGACGAAAACTAAGAAGAT
CAAAGAGGAATACATTGATCAGGAAGAACTAAACAAGACCAAGCCTCTTTGGACCAGAAACCCTGATGACATCATTCAAG
AAGAATATGAAGAATTCTACAAAAGCCTCACCAATGACTGGGAAGACAACTTGGCAGTCAAGCACTTTTCTGTAGAAGGT
CAGTTGGAATTCAGGGCATTGCTATTCATTCCTCATGAGGCTCCCTTTGACCTTTTTGAGAACAAGAAGAAAAAGAACAA
TGTCAAACTCTATGTCCATCATGTATTCATCATGGACAGCTGTGATGAGCTGATACCAGAGTATCTCAACTTTATTCGTG
TTGTGGTTGACTCTGAGGATTTGCCTCTGAACATCTCCCAAGAAATGCTCCAGTAGAGCAAAATCTTGAAAATAATTCGC
AAAACATTGTTAATAAGTGCCTAGTGCTCCTCTCTGAGCTGGCAGAAGACAAGGAGAATTATAGGAAATTCTATGAGGCA
TTCTCTAAAAATCTCAAGCATGGAATTCACGAGGATTCCACTAACCAATGCCACCTGTCTGAGCTGCTGCACGATCACAC
CTCCCAGTCTGGAGATGAGATGACATCTCTGTCAGAGTATGTTTCTCACATAAAGGAGACACAGAAGTCCATCTATTACA
TCACTGGTGAGAGCAAAGAGCAGGTGGCCAACTCAGCTTTTGTGGAGTGAGTGCGGAAGTGGGGCTTCGAGGTGGTATAT
ATGACTGAGCCCATTGACGACTACTGTGTGCAGGAGCTAAAAAAGTTTGATAGGAAGAGCCTGGTCTCAGTTACCAAGGA
GGGTCTGGAGCTACCAGAGGATGAGGAGGAGAAGAAGAAAATGGAAGAGAGCAAGGCAAAGTTTGAGAACCTCTGCAAGC
TCATGAAAGAAATCTTAGATTAGAAGGTTGAGAAGGTGACAATCTCCAATAGGCTTGTGTCTTCACCCTGCTGCATTGTG
ACCAGCACCTATGGCTGGACAGTCAATATGGAATGGATCATGAAAGCCCAGGCACTTCAGGACAACTCCACCATGGGCTA
CATGGTGGCCAGAAAGCACCTGGAAATCAACCCTGAC

Alignment

ORF - retro_cjac_3596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.74 %
• Parental protein coverage: 63.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKERDKEVSDDEESED-KPEIEDVGSVKEKYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDH
          EK.....V..DEE....K.........KE.YIDQEELNKTKP.WTRNPDDI..EEY.EFYKSLTNDWED.
Retrocopy EKPKTEDVGSDEEDDSGKDKKTKTKKIKEEYIDQEELNKTKPLWTRNPDDIIQEEYEEFYKSLTNDWEDN

Parental  LAVKHFSVEGQLEFRALLFVPRRAPFDLFENRKKKNNIKLYVRRVFIMDNCEELIPEYYIYFIRGVVDSE
          LAVKHFSVEGQLEFRALLF.P..APFDLFEN.KKKNN.KLYV..VFIMD.C.ELIPEY...FIR.VVDSE
Retrocopy LAVKHFSVEGQLEFRALLFIPHEAPFDLFENKKKKNNVKLYVHHVFIMDSCDELIPEY-LNFIRVVVDSE

Parental  DLPLNISREMLQQSKILKVIRK-NLVKKCLELFTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSE
          DLPLNIS.EMLQ.SKILK.IRK.N.V.KCL.L..ELAEDKENY.KFYE.FSKN.K.GIHEDS.N...LSE
Retrocopy DLPLNISQEMLQ*SKILKIIRK<NIVNKCLVLLSELAEDKENYRKFYEAFSKNLKHGIHEDSTNQCHLSE

Parental  LLRYYTSASGDEMVSLKDYCTRMKENQKHIYYITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQ
          LL...TS.SGDEM.SL..Y....KE.QK.IYYITGE.K.QVANSAFVE..RK.G.EV.YM.EPID.YCVQ
Retrocopy LLHDHTSQSGDEMTSLSEYVSHIKETQKSIYYITGESKEQVANSAFVE*VRKWGFEVVYMTEPIDDYCVQ

Parental  QLKEFEGKTLVSVTKEGLELPEDEEEKKKQEEKKTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVT
          .LK.F..K.LVSVTKEGLELPEDEEEKKK.EE.K.KFENLCK.MK.IL..KVEKV..SNRLV.SPCCIVT
Retrocopy ELKKFDRKSLVSVTKEGLELPEDEEEKKKMEESKAKFENLCKLMKEILD*KVEKVTISNRLVSSPCCIVT

Parental  STYGWTANMERIMKAQALRDNSTMGYMAAKKHLEINPD
          STYGWT.NME.IMKAQAL.DNSTMGYM.A.KHLEINPD
Retrocopy STYGWTVNMEWIMKAQALQDNSTMGYMVARKHLEINPD

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	0.27 RPM	168.69 RPM
SRP051959_heart	0.35 RPM	217.01 RPM
SRP051959_kidney	0.24 RPM	145.21 RPM
SRP051959_liver	0.43 RPM	269.35 RPM
SRP051959_lung	0.46 RPM	194.35 RPM
SRP051959_lymph_node	0.32 RPM	189.24 RPM
SRP051959_skeletal_muscle	0.57 RPM	221.48 RPM
SRP051959_spleen	0.34 RPM	164.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3596 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3596 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3596 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006270	1 retrocopy	retro_btau_501,
Canis familiaris	ENSCAFG00000018036	1 retrocopy	retro_cfam_1094,
Callithrix jacchus	ENSCJAG00000033945	8 retrocopies	retro_cjac_1818, retro_cjac_2300, retro_cjac_2835, retro_cjac_3514, retro_cjac_3596 , retro_cjac_3601, retro_cjac_3626, retro_cjac_502,
Cavia porcellus	ENSCPOG00000002015	1 retrocopy	retro_cpor_1372,
Homo sapiens	ENSG00000080824	2 retrocopies	retro_hsap_237, retro_hsap_859,
Macaca mulatta	ENSMMUG00000011073	2 retrocopies	retro_mmul_1526, retro_mmul_2313,
Monodelphis domestica	ENSMODG00000013302	3 retrocopies	retro_mdom_1653, retro_mdom_2010, retro_mdom_817,
Mus musculus	ENSMUSG00000021270	1 retrocopy	retro_mmus_2139,
Nomascus leucogenys	ENSNLEG00000015925	3 retrocopies	retro_nleu_714, retro_nleu_822, retro_nleu_854,
Pongo abelii	ENSPPYG00000006153	1 retrocopy	retro_pabe_1760,
Pan troglodytes	ENSPTRG00000006736	2 retrocopies	retro_ptro_207, retro_ptro_596,
Rattus norvegicus	ENSRNOG00000007219	1 retrocopy	retro_rnor_860,