RetrogeneDB ID: retro_cjac_1747

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:28414924..28416473(-)
• Located in intron of: ENSCJAG00000018702

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000016105
• Aliases: None
• Description: None

Sequence

>retro_cjac_1747
ATGTAGGAGCCCGGAGCTACTCCTCAGCCCTACTTGGGGCTGGTCATGGAGAAGCTACACAGGATTGTGGCAGCACTGCT
GGAAAGTATGGTATCAAATTCTAATGGTTTTCCATGGGAATTAGTGATATGGGCAGGTGCTACTGGATTTTTCGCTATTC
CCCTTTTTTTGTGGAGAAGTTTTACATCAGTTAGGAGTTGGCTATATGTGGGAAGACAGAAAAGGTTTGCTGTAGTGCTT
TATGAACAAATTAAAGAAAAATGTAAACTACTTGAAAAATTTAGTTTTGTATAAAAAAGCTATGAAGGCTATGAAATAGA
GTCATCTTTAAAGGATGTCAACTTTGAGAAGGAGGCAGCAGAAGCACAAAGTTTGGAGGCAACCCGTGAAAAGCTGAACA
GGTCCATTTCTGAAATTGAAGATGAAATACTGTACCTCACAAAGGAGTTAAAAGAAGAGAAATATAAACATTCTATACAC
GATGAGTTGATGGCAGATATTTCAAAAATGATACAGTCTCCAGAAGATCAGTCAAAATCCCTAAATCACAAATAGCTGAA
GCCAAAATGCCCTTCAAGATATTTCAAATGAATGGCAAACAACTGAAGATAGTGATAAAAGATGCTTTGAATGAAAATCC
TCAACTTCAGCAAAGCCAGAAACATCTTTTGTAGGAAGCTGAAGTATGGAAAGAACAAGTGAGCGAACTTAATAAACAGA
AAATAACATGTGAAGACTCCAAAGTACACACAGAACAAGTTCTAAATGACAAAGAGGAGCACATCAAGACTCTGACTAAA
CACTTGCTGAAGACGAAAGACTGGGCTGCTATGCTTGGAGAAGACATAATGGATGATAATAACTTGAAAGTAGAAATGAC
CAGTGAATCAGAAAATAGCACTTATTTAGCTGATCCTCCAAAAGGAGCTTTGAAGAAACTGATTCATGCTGCTAAGTTCA
ATGCTTCTTTAAAAATTTTAAAAGGAGAAAGAAACTAAATTTATATTCAGTTGTCCGAAATTGATAAAACAAAGAAGGAG
CTTATGGGGCATATTAAACATCTTTAGTCTGAACAAGCATCTTTGCAGTTAGAAAACACATTTTGAAAGTAAGAATCAGA
AGCTTCAACAGAAACTTGAAGTAATGACTGAATTACATCAAGAAACTACAATGAGACTTTACAAAACACTAACTGTAGAG
GAAAATTACCAGTTAGAGAGACAAGAGAAACTCTCTGAACAAGACAAAAAGGTCAACTATACCACTGACCAGCTGGCAAA
GTATAGAAAGCAAGTCAAATATCTTGAAGAAGAATTGGAAAGAATGATTCTTTCTTATCAAGAGCAGATTTTACTCCTTA
AAAAAAAAAGCAGATGACAATTGTTTGGCAGCTTGGACTGCTGAAAGAAACCTCAATGGCTTAAGGAAAGAAAATGCTAA
ATACAGACACAAATTAACTGACACAGAGATTAAACTCAAATTTTTACACAAAGATCCTTCTGCAGTTGATGTTCCAAACA
CAGGATTTGGCAGAGAGTATTACACATAT

Alignment

ORF - retro_cjac_1747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.6 %
• Parental protein coverage: 64.55 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEEPGATPQPYLGLVLEELRRVVAALPEGMRPDSNPYGFPWELVICAAVVGFCAVLFFLWRSFRSVRSRL
          M.EPGATPQPYLGLV.E.L.R.VAAL.E.M...SN..GFPWELVI.A...GF.A...FLWRSF.SVRS.L
Retrocopy M*EPGATPQPYLGLVMEKLHRIVAALLESMVSNSN--GFPWELVIWAGATGFFAIPLFLWRSFTSVRSWL

Parental  YVGREKKLAVMLSGLIEEKCKLLEKFSLVQKEYEGYEVESSLKDASFEKEATEAQSLEATCEKLNRSNSE
          YVGR.K..AV.L...I.EKCKLLEKFS.V.K.YEGYE.ESSLKD..FEKEA.EAQSLEAT.EKLNRS.SE
Retrocopy YVGRQKRFAVVLYEQIKEKCKLLEKFSFV*KSYEGYEIESSLKDVNFEKEAAEAQSLEATREKLNRSISE

Parental  LEDEILCLEKELKEEKSKHSEQDELMADISKRIQSLEDESKSI-KSQVAEAKMTFKIFQMNEERLRIAIK
          .EDEIL.L.KELKEEK.KHS..DELMADISK.IQS.ED.SKS..KSQ.AEAKM.FKIFQMN...L.I.IK
Retrocopy IEDEILYLTKELKEEKYKHSIHDELMADISKMIQSPEDQSKSL<KSQIAEAKMPFKIFQMNGKQLKIVIK

Parental  DALNENSQLQESQKQLLQEAEVWKEQVSELNKQKITFEDSKVHAEEVLNDKENHIKILTERLIKMKDWAA
          DALNEN.QLQ.SQK.LL.EAEVWKEQVSELNKQKIT.EDSKVH.E.VLNDKE.HIK.LT..L.K.KDWAA
Retrocopy DALNENPQLQQSQKHLL*EAEVWKEQVSELNKQKITCEDSKVHTEQVLNDKEEHIKTLTKHLLKTKDWAA

Parental  ILGEEITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQIYIQLSDVDKTKEE
          .LGE.I.DD.NL..EM.SESEN..YL..PPKGALKKLIHAAK.NASLK.L.GERN.IYIQLS..DKTK.E
Retrocopy MLGEDIMDDNNLKVEMTSESENSTYLADPPKGALKKLIHAAKFNASLKILKGERN*IYIQLSEIDKTKKE

Parental  LTEHIKNLQTEQASLQSENTHFESENQ-KLQQKLK-VMTELYQENEMKLHRKLTVEENFRLEKEEKLCKV
          L..HIK.L..EQASLQ.ENT....E........LK.VMTEL.QE..M.L...LTVEEN..LE..EKL...
Retrocopy LMGHIKHL*SEQASLQLENTF*K*ESE<SFNRNLK<VMTELHQETTMRLYKTLTVEENYQLERQEKLSEQ

Parental  DEKISHATEELETYRKRAKDLEEELERTIHSYQGQII-SHEKKAHDNWLAARTAERNLNDLRKENAHNRQ
          D.K....T..L..YRK..K.LEEELER.I.SYQ.QI..S..KKA.DN.LAA.TAERNLN.LRKENA..R.
Retrocopy DKKVNYTTDQLAKYRKQVKYLEEELERMILSYQEQIL>SLKKKADDNCLAAWTAERNLNGLRKENAKYRH

Parental  KLTETELKFELLEKDPYALDVPNTAFGREHSPY
          KLT.TE.K...L.KDP.A.DVPNT.FGRE...Y
Retrocopy KLTDTEIKLKFLHKDPSAVDVPNTGFGREYYTY

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	1.42 RPM	25.65 RPM
SRP051959_heart	1.25 RPM	22.82 RPM
SRP051959_kidney	0.98 RPM	127.75 RPM
SRP051959_liver	1.21 RPM	139.82 RPM
SRP051959_lung	2.80 RPM	25.96 RPM
SRP051959_lymph_node	2.88 RPM	24.68 RPM
SRP051959_skeletal_muscle	0.50 RPM	20.96 RPM
SRP051959_spleen	3.89 RPM	23.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1747 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1747 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1747 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016105	4 retrocopies	retro_cjac_1747 , retro_cjac_2711, retro_cjac_3217, retro_cjac_921,
Cavia porcellus	ENSCPOG00000026514	2 retrocopies	retro_cpor_189, retro_cpor_727,
Homo sapiens	ENSG00000150527	3 retrocopies	retro_hsap_1201, retro_hsap_3691, retro_hsap_640,
Homo sapiens	ENSG00000258941	1 retrocopy	retro_hsap_78,
Gorilla gorilla	ENSGGOG00000011990	1 retrocopy	retro_ggor_936,
Nomascus leucogenys	ENSNLEG00000004121	10 retrocopies	retro_nleu_1218, retro_nleu_1690, retro_nleu_2087, retro_nleu_2103, retro_nleu_2148, retro_nleu_2600, retro_nleu_2951, retro_nleu_3017, retro_nleu_3077, retro_nleu_688,
Pongo abelii	ENSPPYG00000005768	9 retrocopies	retro_pabe_1001, retro_pabe_1002, retro_pabe_1007, retro_pabe_1055, retro_pabe_1060, retro_pabe_1588, retro_pabe_2119, retro_pabe_29, retro_pabe_3024,
Pan troglodytes	ENSPTRG00000006297	10 retrocopies	retro_ptro_1286, retro_ptro_1712, retro_ptro_2503, retro_ptro_2580, retro_ptro_2880, retro_ptro_466, retro_ptro_821, retro_ptro_826, retro_ptro_868, retro_ptro_876,
Ictidomys tridecemlineatus	ENSSTOG00000015890	1 retrocopy	retro_itri_95,