RetrogeneDB ID: retro_cjac_3217

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:52290982..52292790(+)
• Located in intron of: None

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_3217
GTGGAGGAGCCCCAGGCTACCCCTCAGCCATACTTGAGGCTCCTTCTGGAGATGCAACACAGGGTTGTAGCAGCACTGCG
CTAAAGTTTGGGAGCAGATTCTAATTCTTATGGTTTTCCATGGGAATGGGTGATATGGGCAGCTATTTTTTGATTTATTG
CTGTTCTCTTTTTTTTGTGGAGAGGTTTTAGATCAGTTAGGAGTCAGCTTTATTCGGGAAGAGAGAAAGAGCTTGCTGAA
ACACTTTCTACACTAATTCAAGAAAAATGTAAACTACTGGAAAAACTGAGTATTATTCAAAAAGAGTATGAAGGCCATGA
AGTAGAGTCATCTTTAAAGGATGCTAGCTTTGAGAAGGAGGCAACAGAAGCACAAAGCTTGGAGGCAACCTGTGCAAAGC
TGAACAGGTCCAATGTGGAACTTGAGGAAGAAATACTATGTCTAGTAAAAGAGTTAAAAGAGAGAAATTGAAACAGTTGG
AACAAAATGAACCGATGGCGGATATTTCAAAAAGGATACAGTCTCTAGAAGATGAGTCAAAATCCCTCAAATCACCAGTA
GCTGAAGCCAAAATGACCTTCAAGACTTTATTTCCAATGAAATGAGAACCACTGAAGACAGCAATAAAAGATGCTTTGGA
TGAAAATTCTCAGCTTCGGGAAAGCCAGAAACAGCTTTTGCAAGAAACTGAAGTTTGGAAAGAACAAGTGAGTGAACTTA
ATAAACAGAAAATAACATTGGAAGACTCCAAAGTACACGCAGAACAAGTTCTCAGTACTAAAGACAATCACATCAAGACT
CTGACTAAACACTTGCTGAAGATGAAAGATTGGGCAGCTATGCTTGGAGAAGACAAAATGGATGAAGGTAACTTGGAGTC
AGAAATGAACAGTGAATCAGAAAATGGTGTGTACTTAGATCATCCTCCAAACAGAGCTTTGAAGAAACTGATTCATGCTG
CTAAGTTCAATGCTTCTTTTAAAAGCTTAGAAGGAGAAAGATCCCAAATTTATATTCAGTGATCTGAAGTTGATAAAATG
AAGGAAGAGCTTACTGAATGTATTAAAAATCTTGAGATTGAACTTGCATCTTTGCAGTCAGAAAACACACATTTTGAAAG
TGAGAATCAGAAGCTTCAACAGAAACTTCAAGTAATAACCGAATTATATCAAGAAAATGAAATGAAACTTTACAGGAAAT
TAACAACAGAGGAAAATTGCCGTTTAGAGAGAGAAGAGAAACTTTCTAAGGTAGACTAAAGGATCAGCCATGCTACAACC
AAGCTGGAGACCTATAGAAAGAGAGCCAAAGATCTTGAAGAAGAGTTGGAGAGAACAATGCATTATTATTAAAAGCACAG
TATTTCCAATGAGAACAATGTACATGGTAATTGGTTTGCAGCTTGAACTGCTGAAAAAAATCTCAATAATTTAAGGAAAG
AAAATGCTCACACAGAGAAAAATTAACTGAACTACTGCTTAAATTTGAACTTTTAGAAAAAAATATGCATGCAGTGGATG
TTCCAAATACACCATTTGGCAGAGAACCTTCCTCATATGGCTTCTCACCACTGGGTCTGCCTTCATATGAAATGAGAGCT
TTTCTGTCTCCTCGCAACTTCATTGGAGGCTCTACCCAGACTCTCACCTTTGCTCACAAAGAGAGAAGGAAGCGGCTCAA
GACGCCCAGGGAATCCACTGGACCATCAGATTACCAACGAAAGAGGAGAATCAAGCTCTGATATGTTAACTGATTCTCAC
AGGGGTCCTTCTGACACTGGGCCCCTGTCACCTCTGTGGGAAAGGGAG

Alignment

ORF - retro_cjac_3217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.41 %
• Parental protein coverage: 74.88 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEEPGATPQPYLGLVLEELRRVVAALPEGMRPDSNPYGFPWELVICAAVVGFCAVLFFLWRSFRSVRSRL
          .EEP.ATPQPYL.L.LE...RVVAAL......DSN.YGFPWE.VI.AA...F.AVLFFLWR.FRSVRS.L
Retrocopy VEEPQATPQPYLRLLLEMQHRVVAALR*SLGADSNSYGFPWEWVIWAAIF*FIAVLFFLWRGFRSVRSQL

Parental  YVGREKKLAVMLSGLIEEKCKLLEKFSLVQKEYEGYEVESSLKDASFEKEATEAQSLEATCEKLNRSNSE
          Y.GREK.LA..LS.LI.EKCKLLEK.S..QKEYEG.EVESSLKDASFEKEATEAQSLEATC.KLNRSN.E
Retrocopy YSGREKELAETLSTLIQEKCKLLEKLSIIQKEYEGHEVESSLKDASFEKEATEAQSLEATCAKLNRSNVE

Parental  LEDEILCLEKELKE-EKSKHSEQDELMADISKRIQSLEDESKSIKSQVAEAKMTFK-IFQMNEERLRIAI
          LE.EILCL.KELKE.EK.K..EQ.E.MADISKRIQSLEDESKS.KS.VAEAKMTFK..F.M..E.L..AI
Retrocopy LEEEILCLVKELKE<EKLKQLEQNEPMADISKRIQSLEDESKSLKSPVAEAKMTFKTLFPMK*EPLKTAI

Parental  KDALNENSQLQESQKQLLQEAEVWKEQVSELNKQKITFEDSKVHAEEVLNDKENHIKILTERLIKMKDWA
          KDAL.ENSQL.ESQKQLLQE.EVWKEQVSELNKQKIT.EDSKVHAE.VL..K.NHIK.LT..L.KMKDWA
Retrocopy KDALDENSQLRESQKQLLQETEVWKEQVSELNKQKITLEDSKVHAEQVLSTKDNHIKTLTKHLLKMKDWA

Parental  AILGEEITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQIYIQLSDVDKTKE
          A.LGE...D..NLE.EMNSESENG.YLD.PP..ALKKLIHAAK.NAS.K.LEGER.QIYIQ.S.VDK.KE
Retrocopy AMLGEDKMDEGNLESEMNSESENGVYLDHPPNRALKKLIHAAKFNASFKSLEGERSQIYIQ*SEVDKMKE

Parental  ELTEHIKNLQTEQASLQSENTHFESENQKLQQKLKVMTELYQENEMKLHRKLTVEENFRLEKEEKLCKVD
          ELTE.IKNL..E.ASLQSENTHFESENQKLQQKL.V.TELYQENEMKL.RKLT.EEN.RLE.EEKL.KVD
Retrocopy ELTECIKNLEIELASLQSENTHFESENQKLQQKLQVITELYQENEMKLYRKLTTEENCRLEREEKLSKVD

Parental  EKISHATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHDNWLAARTAERNLNDLRKENAH-NRQK
          ..ISHAT..LETYRKRAKDLEEELERT.H.Y....IS.E...H.NW.AA.TAE.NLN.LRKENAH..R.K
Retrocopy *RISHATTKLETYRKRAKDLEEELERTMHYY*KHSISNENNVHGNWFAA*TAEKNLNNLRKENAH<HREK

Parental  LTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGRPSSETRAFLSP-PTLLEGPLRLSPLLPGGGG
          LTE..LKFELLEK...A.DVPNT.FGRE.S.YG.SPLG.PS.E.RAFLSP..T.LE...RLSPLL....G
Retrocopy LTELLLKFELLEKNMHAVDVPNTPFGREPSSYGFSPLGLPSYEMRAFLSP>ATSLEALPRLSPLLTKREG

Parental  RGPRGPGNPLDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWEQD
          .G.R.PGNPLDHQITNERGESS.D.LTD.HR.PSDTG.LSP.WE..
Retrocopy SGSRRPGNPLDHQITNERGESSSDMLTDSHRGPSDTGPLSPLWERE

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	0.00 RPM	25.65 RPM
SRP051959_heart	0.00 RPM	22.82 RPM
SRP051959_kidney	0.00 RPM	127.75 RPM
SRP051959_liver	0.00 RPM	139.82 RPM
SRP051959_lung	0.00 RPM	25.96 RPM
SRP051959_lymph_node	0.00 RPM	24.68 RPM
SRP051959_skeletal_muscle	0.00 RPM	20.96 RPM
SRP051959_spleen	0.00 RPM	23.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3217 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3217 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,