RetrogeneDB ID: retro_cjac_2711

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:32297550..32299095(+)
• Located in intron of: ENSCJAG00000010218

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_2711
GAGCCTGGAGCTACTCCTCAGCCCTAGTTGGGGCTGGTCATGGAGAAGCTACACAGGATCGTGGCAGCACTGCTGGAAAG
TATGGTATCAAATTCTAATGGTTTTCCATGGGAATTAGTGATATGGGCAGGTGTTATTGGACTTTTTGCTATTCCCCTTT
TTTTGTGGAGAAGTTTTAGATCAGTCAGGAGTTGGCTATATGTGGGGAGAGAGAAAAAGCTTGCTGTAATGCTTTGTGAG
CAAATTAAAGAAAAATGTAAACTACTTGAAAAATTAAGTTTTCTACAAAAAAGCTATGAAGGCTATGAAAGAGAGTTATC
TTTACAGGACGTCAGCTTTGAGAAGGAAGCAGCAGAAGCACAAAGTTTGGAGGCAACCTGTGAAAAGCTAAGCAGGTCCA
TTTCTGAAATACAGGATGAAATATCACATCTAAAAAAAGAGTTAAAAGAAGAGAAATACAAACATTCTAGACAACATCCA
TTGATGGTGGATACTTCAGAAATTAGACAGTCTCTAGAAGATCTGTCAAAATCCCTCAAATCACAACTAGCTGAAGCCAA
AATGCCCTTGAACATATTTCAAATGAATGGTGAACAACTGAAGACAGAGATAAAAGATGCTTTGAATGAAAATTCTCAAC
TTCAGGAAAGCCAGAAACATCTTTTGCAAGAAGCTGAAGTAGGGAAAGAACAAGTGAGTGAACTTAATAAACAGAAAATA
ATATTTGAAGACTCCAAAGTACACGCAGAACAAGTTCTAAATGACAAAGACGATCACATCAAGACGCTGACTGAACACTT
GCTGAAGATGAAAGATTGGGCTGCTGTGCTTGGAGAAGACATGATGGATGATCATAACTCGAAAGTAGAAATGAAGAGTG
AATCAGAAAACGGCGCTTCCTTAGCTAATCCTCGGAAAGGAGCTTTGAAGAAACTGATGCATGCTGCTGAGTTAAATGCT
TCTTTCAAAAGTCTAGAAGGAGAAAGAAATGAAATTTACATTCAGCTGTCCGAAACTGAGAAAACAGAGAAGCAGCTTAT
GGGGCATATTAAACATCTTCAGTCTGAACAAGCATCTTTGCAGTCAGAAAACACAGATTTTGAAAGTGAGAATCAGAAGC
TTCAACAGAAACTTCAAGTAATGACTGAATTACATGAAGAAACGACAATGAGACTTTACAAAACATTCACTGTAGAGGAA
AATTACCAGTTAGAGAGACAAGAGAAACTTTCTAAACAAGACGAAAAGGTCAACTCTACCACTGACCAGCTGGACGAGTA
TAGAAAGCAAGCCCAACATCTTGAAGAGGAGTTGGAAAGAATGATTCTTTCTTATCAAGAGCAGATTTTACTCCTTAAGA
AAAAAGCACATGACAATTGGTTGGCAGCTCGGACTGCTGAAATAAACCTCGACCGATTAAGGAAAGAAAATGCTAAGTAC
AGACGAAAATTAACTGACACAGAGATGAAATTTAAATTTTTACACAAAGATCCTGCTGCAGTTGATGTTCCAAACACAGG
ATTTGGCAGAAAGCATTACACGTAT

Alignment

ORF - retro_cjac_2711 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.18 %
• Parental protein coverage: 64.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPGATPQPYLGLVLEELRRVVAALPEGMRPDSNPYGFPWELVICAAVVGFCAVLFFLWRSFRSVRSRLYV
          EPGATPQP.LGLV.E.L.R.VAAL.E.M...SN..GFPWELVI.A.V.G..A...FLWRSFRSVRS.LYV
Retrocopy EPGATPQP*LGLVMEKLHRIVAALLESMVSNSN--GFPWELVIWAGVIGLFAIPLFLWRSFRSVRSWLYV

Parental  GREKKLAVMLSGLIEEKCKLLEKFSLVQKEYEGYEVESSLKDASFEKEATEAQSLEATCEKLNRSNSELE
          GREKKLAVML...I.EKCKLLEK.S..QK.YEGYE.E.SL.D.SFEKEA.EAQSLEATCEKL.RS.SE..
Retrocopy GREKKLAVMLCEQIKEKCKLLEKLSFLQKSYEGYERELSLQDVSFEKEAAEAQSLEATCEKLSRSISEIQ

Parental  DEILCLEKELKEEKSKHSEQDELMADISKRIQSLEDESKSIKSQVAEAKMTFKIFQMNEERLRIAIKDAL
          DEI..L.KELKEEK.KHS.Q..LM.D.S...QSLED.SKS.KSQ.AEAKM...IFQMN.E.L...IKDAL
Retrocopy DEISHLKKELKEEKYKHSRQHPLMVDTSEIRQSLEDLSKSLKSQLAEAKMPLNIFQMNGEQLKTEIKDAL

Parental  NENSQLQESQKQLLQEAEVWKEQVSELNKQKITFEDSKVHAEEVLNDKENHIKILTERLIKMKDWAAILG
          NENSQLQESQK.LLQEAEV.KEQVSELNKQKI.FEDSKVHAE.VLNDK..HIK.LTE.L.KMKDWAA.LG
Retrocopy NENSQLQESQKHLLQEAEVGKEQVSELNKQKIIFEDSKVHAEQVLNDKDDHIKTLTEHLLKMKDWAAVLG

Parental  EEITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQIYIQLSDVDKTKEELTE
          E...DD.N...EM.SESENGA.L.NP.KGALKKL.HAA.LNAS.K.LEGERN.IYIQLS...KT...L..
Retrocopy EDMMDDHNSKVEMKSESENGASLANPRKGALKKLMHAAELNASFKSLEGERNEIYIQLSETEKTEKQLMG

Parental  HIKNLQTEQASLQSENTHFESENQKLQQKLKVMTELYQENEMKLHRKLTVEENFRLEKEEKLCKVDEKIS
          HIK.LQ.EQASLQSENT.FESENQKLQQKL.VMTEL..E..M.L....TVEEN..LE..EKL.K.DEK..
Retrocopy HIKHLQSEQASLQSENTDFESENQKLQQKLQVMTELHEETTMRLYKTFTVEENYQLERQEKLSKQDEKVN

Parental  HATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHDNWLAARTAERNLNDLRKENAHNRQKLTETE
          ..T..L..YRK.A..LEEELER.I.SYQ.QI....KKAHDNWLAARTAE.NL..LRKENA..R.KLT.TE
Retrocopy STTDQLDEYRKQAQHLEEELERMILSYQEQILLLKKKAHDNWLAARTAEINLDRLRKENAKYRRKLTDTE

Parental  LKFELLEKDPYALDVPNTAFGREHSPY
          .KF..L.KDP.A.DVPNT.FGR.H..Y
Retrocopy MKFKFLHKDPAAVDVPNTGFGRKHYTY

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	0.02 RPM	22.82 RPM
SRP051959_kidney	0.02 RPM	127.75 RPM
SRP051959_liver	0.02 RPM	139.82 RPM
SRP051959_lung	0.02 RPM	25.96 RPM
SRP051959_lymph_node	0.05 RPM	24.68 RPM
SRP051959_skeletal_muscle	0.02 RPM	20.96 RPM
SRP051959_spleen	0.02 RPM	23.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2711 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2711 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2711 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,