RetrogeneDB ID: retro_cjac_2300

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:178065194..178066531(-)
• 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_2300
ATCAAAGAGAAATACATTGATCAGGAAGAACTAAACAAGACCAAGCCTATTTGGACCAGAAACCCTGATGACATCACCCA
AGAGGAGTATGGAGAATGCTAAAAGAGCTTCACCAATGACTGAGAAGACCCCTGGCAGTACAAGCAATTGCTGTAGAAGG
TCAGTTGGAATTCAGGGCATTGTTATTCATTCCTTGCCGGGTTTTCTTTGACCTCTTTTAGAACAAGAAGAAAAAAGAAC
ATCAAACTTCATGTCCATCATGCGTTCATCATGGACAGCTGTGAGGAGCTGATACCAGTGTATCTCAACTGTATCTGTGG
TGTGGTCTGCCCCTGAACATCTCCCAAGAAATGCTCTAGCAGAGAAAAATCTTGAAAGTCATTCTCAGAAACATTGTTAA
GAAGTGCCTTGAGCTCTTCTCTGAGCTGGTGGAAGACAAGGAGAATTACAAGAAATTCTATGAGGCATTCCCTAAAAATC
TCAAGCTTAGAATACATGAGGACTCTACTAACTGATGCCACCTATCTGAGCTGCTGCACTATCAGGCCTCCCAGTCTGGA
GATGAGATGATATCTCTGTCAGAGTATGTTTCTCGCATGAAGGAGACACAGAAATCCATCTATTACTTCACTGGTGAGAG
CAAAGAGCAGGTGGCCAACTCAGGTTTTGTGGAGTGAGTGCAGAAGTGGGACTTCAAGGTGGTATATATGAGAGAGCCCA
TTGATGAGTACTATGTGCAGCAGCTCAAAGAGTTTGATGGGAAGAGCCTGGTCTCAGTTACCAAGGAGGGTCTGGAGTTA
CCTGAGGATGAGGAGGAGAAGAAAAAAATGGAAGAAAGCAAGGCAAAGTTTGAGAACATTTGCAAGTTCATGAAAGAAAT
CTTAGATAAGAAGATTGAGAAGGTGACAATCTCCAATAGGCTTGTCTTCACCCTGCTGCACTGTGACCAGCACCTACAGC
TGGATAGCCAATATGGAGTGGATCATGAAAGCCCAGGTACTTCGGGACAACACTATCATGGCTATATGATGGCCAAAAGG
CACCTGGAGATCAACCCCGACCACCCCATTGTGAGACGCCGTCACAGAAAGCTGAGACAGACAAGAATGACAAGGCAGTC
AAAGACTTGACGGTGCTGCGGTTTGAAACCACCCTGCTGTCTTCTGGCTTTTCCCTTGAAGATCCCCTGACCCACTCCAA
CCACATCCACTGTATGATCAAGCTAGGTCTAGGTATCTATGAAGACGAAGTGGCAGCAGAGGAACCCAGTGCTGCGGTTC
CTGATGAGATTCCCCACTCCTGAGGGTGATGAGGATGCATCTTGCATGAAAGAAGTC

Alignment

ORF - retro_cjac_2300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.21 %
• Parental protein coverage: 74.75 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  VKEKYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDH-LAVKHFSVEGQLEFRALLFVPRRAP
          .KEKYIDQEELNKTKPIWTRNPDDIT.EEYGE..KS.TND.ED..LAV....VEGQLEFRALLF.P.R..
Retrocopy IKEKYIDQEELNKTKPIWTRNPDDITQEEYGEC*KSFTND*EDP<LAVQAIAVEGQLEFRALLFIPCRVF

Parental  FDLFEN-RKKKNNIKLYVRRVFIMDNCEELIPEYYIYFIRGVV-DSEDLPLNISREMLQQSKILK-VIRK
          FDLF.N.R.KKN.IKL.V...FIMD.CEELIP..Y...I.GVV...E.LP.N...E....S...K....K
Retrocopy FDLF*N>RRKKN-IKLHVHHAFIMDSCEELIP-VYLNCICGVV>APEHLPRNALAEKNLESHSQK>IVKK

Parental  NLVKKCLELFTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASGDEMVSLKDYCTRM
          .L.....EL.......K..Y..F.....KN.KL.IHEDS.N...LSELL.Y..S.SGDEM.SL..Y..RM
Retrocopy CL-ELFSELVEDKENYKKFYEAF----PKNLKLRIHEDSTN*CHLSELLHYQASQSGDEMISLSEYVSRM

Parental  KENQKHIYYITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQQLKEFEGKTLVSVTKEGLELPED
          KE.QK.IYY.TGE.K.QVANS.FVE...K....V.YM.EPIDEY.VQQLKEF.GK.LVSVTKEGLELPED
Retrocopy KETQKSIYYFTGESKEQVANSGFVE*VQKWDFKVVYMREPIDEYYVQQLKEFDGKSLVSVTKEGLELPED

Parental  EEEKKKQEEKKTKFENLCKIMKDILEKKVEKVVVSNRLV-TSPCCIVTSTYGWTANMERIMKAQALRDNS
          EEEKKK.EE.K.KFEN.CK.MK.IL.KK.EKV..SNRLV....C...TSTY.W.ANME.IMKAQ.LRDN.
Retrocopy EEEKKKMEESKAKFENICKFMKEILDKKIEKVTISNRLV>SPCCTV-TSTYSWIANMEWIMKAQVLRDNT

Parental  TM-GYMAAKKHLEINPDHSII-ETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLEDPQTHANRIYRM
          .M.GYM.AK.HLEINPDH.I..ET..QKAE.DKNDK.VKDL..L..ET.LLSSGFSLEDP.TH.N.I..M
Retrocopy IM<GYMMAKRHLEINPDHPIV<ETPSQKAETDKNDKAVKDLTVLRFETTLLSSGFSLEDPLTHSNHIHCM

Parental  IKLGLGIDEDDPTADDTSAAVTEEM-PPLEGDDDTSRMEEV
          IKLGLGI.ED...A...SAAV..E..P..EGD.D.S.M.EV
Retrocopy IKLGLGIYEDEVAAEEPSAAVPDEI>PTPEGDEDASCMKEV

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	0.09 RPM	168.69 RPM
SRP051959_heart	0.11 RPM	217.01 RPM
SRP051959_kidney	0.07 RPM	145.21 RPM
SRP051959_liver	0.17 RPM	269.35 RPM
SRP051959_lung	0.13 RPM	194.35 RPM
SRP051959_lymph_node	0.11 RPM	189.24 RPM
SRP051959_skeletal_muscle	0.13 RPM	221.48 RPM
SRP051959_spleen	0.25 RPM	164.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2300 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2300 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,