RetrogeneDB ID: retro_cjac_1818

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:81249966..81251321(+)
• 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_1818
ATCAAAGAGAAATACATTGATCAGGAAGAACTAAACAAGACCAAGCCTATTTGGACTAGAAACCCTGATGACCTCACACA
AGAGGAGTATGGAGAATTCTACAAAAGCCTCACCAATGACCGGGAAGACCACTTGGCAGTCAAGCACTTTTCTGTAGAAG
GTCATTTGGAATTCAGGGCATTGCTATTTATTCCTCGTCGGGCTCCCTTTGACCTTTTTGCGACCAAGAAGAAAAAGAAC
AACATCAAACTCTATGTCCATCGTATATTCAACATGGACGGCTGTGATGAGTTGATACCAGAGTATCTCAACTTTATCAG
TGGTGTGGTTGAATCTGAGGATTTGCCTTTGAACATCTCCCAAGAAATGCTCCAACAGAGCAAAATCTTGAAAGTCGTTC
ACAAAAACATTGTTAAGAAGTGCCTTGAGCTCTTCTCTGAGCTGGGGGAAGACAAGGAGAATTACAAGAAATTCTATGAG
GCATTCTCTAAAAATCTCAAGCTTGGAATTCACGAGGATTCCACTAACAGACGCCGCCTGCCTGAGCTGCTGCGCTATCA
CACCTCCCAGTCTGGAGATGAGATGACATCTCTGTCAGAGTATGTTTCTCACATGAAGGAGACACAGAAGTTCATCTATT
ACATCACTGGTGAGAGCAAAGAGCAAGTGGCCAACTCAGCTTTTGTGGAGTGAGTGCGGAAGCAGGGCCTCAAGGTGGTA
TATATGACTGAGCCCATTGACGAATACTGTGTGCAGCAGCAAGCAGTTTGATGGGAAGAGCCTGGTCTCAGTTACCAAGG
AGGGTCTGGAGCTACTGGAGGGTGAGGAGGAGAAGAAGAAAATGGAAGAGAGCAAGGCAAAGTTTGAGAACCTCTGCAAG
CTCATGAAGGAAATGTTAGATAAGAAGGTTGAGAAGGTGACAATCTCCAATAGGCTTGTGTCTTCACCCTGCTGCATTGT
GACCAGCACCTACGGCTGGACAGCCAATATGGAGCGGATCGTGAAAACCCAGGCACTTCAGGACAACTCCACCATGGGCT
ACATGATATCCAAAAAGCACCTGGAGATCAATCTTGACCACCCATTGTGGAGATGCTGCGGCAGAAGGCTGAGGCAGACA
AGAATGACAAGGCAGTCAAGGACCTTCCGGTGCTGCTGTTTGACACTATCCTGCTCTCTTCTGGCTTTTCCCTTGAGGAT
CCCCAGACCCTCTCCAACCACATCTACCGCATGATCAAGTTAGGTCTAGGTATCGATGAAGATGAAGTGGCAGCAGAGGA
ACCCAGTGCTGCAGTTCCTGATGAGATCCCTCCTCTTGAGGGTGATGAGGATGCATCTACATGGAAGAAGTAGAT

Alignment

ORF - retro_cjac_1818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.81 %
• Parental protein coverage: 74.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VKEKYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFVPRRAPF
          .KEKYIDQEELNKTKPIWTRNPDD.T.EEYGEFYKSLTND.EDHLAVKHFSVEG.LEFRALLF.PRRAPF
Retrocopy IKEKYIDQEELNKTKPIWTRNPDDLTQEEYGEFYKSLTNDREDHLAVKHFSVEGHLEFRALLFIPRRAPF

Parental  DLFENRKKKNNIKLYVRRVFIMDNCEELIPEYYIYFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVK
          DLF...KKKNNIKLYV.R.F.MD.C.ELIPEY...FI.GVV.SEDLPLNIS.EMLQQSKILKV..KN.VK
Retrocopy DLFATKKKKNNIKLYVHRIFNMDGCDELIPEY-LNFISGVVESEDLPLNISQEMLQQSKILKVVHKNIVK

Parental  KCLELFTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKENQ
          KCLELF.EL.EDKENYKKFYE.FSKN.KLGIHEDS.NR..L.ELLRY.TS.SGDEM.SL..Y...MKE.Q
Retrocopy KCLELFSELGEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLPELLRYHTSQSGDEMTSLSEYVSHMKETQ

Parental  KHIYYITGETKDQVANSAFVERLRKHGLEVIYM-IEPIDEYCVQQLKEFEGKTLVSVTKEGLELPEDEEE
          K.IYYITGE.K.QVANSAFVE..RK.GL.V.YM...P.....V...K.F.GK.LVSVTKEGLEL.E.EEE
Retrocopy KFIYYITGESKEQVANSAFVE*VRKQGLKVVYM>LSPLTN-TVCSSKQFDGKSLVSVTKEGLELLEGEEE

Parental  KKKQEEKKTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVTSTYGWTANMERIMKAQALRDNSTMGY
          KKK.EE.K.KFENLCK.MK..L.KKVEKV..SNRLV.SPCCIVTSTYGWTANMERI.K.QAL.DNSTMGY
Retrocopy KKKMEESKAKFENLCKLMKEMLDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIVKTQALQDNSTMGY

Parental  MAAKKHLEINPDH-SIIETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLEDPQTHANRIYRMIKLGL
          M..KKHLEIN.DH..I.E.LRQKAEADKNDK.VKDL..LL..T.LLSSGFSLEDPQT..N.IYRMIKLGL
Retrocopy MISKKHLEINLDH<PIVEMLRQKAEADKNDKAVKDLPVLLFDTILLSSGFSLEDPQTLSNHIYRMIKLGL

Parental  GIDEDDPTADDTSAAVTEEMPPLEGDDDTSR-MEEVD
          GIDED...A...SAAV..E.PPLEGD.D.S..MEEVD
Retrocopy GIDEDEVAAEEPSAAVPDEIPPLEGDEDAST<MEEVD

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	0.07 RPM	168.69 RPM
SRP051959_heart	0.11 RPM	217.01 RPM
SRP051959_kidney	0.02 RPM	145.21 RPM
SRP051959_liver	0.11 RPM	269.35 RPM
SRP051959_lung	0.10 RPM	194.35 RPM
SRP051959_lymph_node	0.05 RPM	189.24 RPM
SRP051959_skeletal_muscle	0.11 RPM	221.48 RPM
SRP051959_spleen	0.04 RPM	164.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1818 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1818 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1818 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,