RetrogeneDB ID: retro_cjac_644

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:185997476..185998826(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021798
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSCJAG00000021414
• Aliases: None
• Description: None

Sequence

>retro_cjac_644
ATGTCTCACCTACTGATGAAACTCCTGCACAAGAAGATCAAGAAGCCAAACCTCAAATTGCAGCAGCGGAACCTAAAGTT
GAAGGGAGACTCAAATCTGACCTTATCAGAAACTGAAAATGGAGTTGTATCTGAAGAAACAATGGGAGGTAGAAAGGATA
AAAAATCAAAACATTCTATGAATCTGGGCCTGTCAGAAGCTCAAAATGGAGATGTGTCTCAAGAAGCAGTGGAAATTTTT
AAAGTTTTTAAATCTCTCCAGAAATCTGCTGTATTAACTAATGGAGAAGCAGCAATGCAGTCTCCCAATTCAGAATCAAA
AAAGAAGAAGAAGAAAAAGAGAAAAATGGTGAACGATGCTGGGCCTGATACAAAAAAAAAAAAAGCCAAAACTGAAAACA
AAGGGGAATCTGAAGAACAAATTGCCTAGACTCCTAAAGAAACAGAAAATAATGTGGAGAAGCCAGATAACGATGAAGAT
GACAGTGAGGTGCCCAGCCTGCCCCTGGAACTGACGGGAGCTTTTGAGGACACCTCATTTGCTTCTCTATGTAATCTGGT
CAATGAAAACACTCTGAAGGCAGTAAAAGAAACAGGTTTACAAACATGACTAAAATTCAGCATAAAAGTATCAGACCACT
TCTGAAGACAGGGATCTTCTAGCAGCTGCAAACACAGGCAGTGGTAAAACCCTGGCTTTCCTCGTCCCTGCAATTGAATT
CATTAAGTTAAAGGTTATGCCCAGGAATGGAACGGGAGTCCTTATTCTCTCACCTGCTAGAGAACTGGCCATGCAAATTT
TGGTGTTCTTAAGGAGCTAATCACTCACCAGGTGCATACCTAGGGGATGATAATGGGTGGCAGTAACAGATCTGCTGAAA
CACAGAAACTTACTAATGGGATCAACATCACTGTGACTACACCAGGTCACCTGCTGGACCATATGCAAAATACCCCAGGG
TTTATGCATAAAAACCTGCAGTGTCTGGTTATTGATGAAGCTGATTGTATCTTGGATGTTGGGTTTGAAGATGAATTAAA
GCAAATTATTAAACTTTTGCCAACACATAGACAGACTGTGCTCTTTTCTACTACCCAAACTCGAAAAGTTGAAGACCTGG
CAAGGATTTCTCTGCAAAGGAGCCCATTGTATGGTGTTATGATGATAAAACTAATGAACAGTGGATGGTCTTGAGCAGGG
ATATATTGTTTGTCCTTTGAAAAGAGATTCCTTCTGCTCTTTACATTCCTTAAGGAGAACCAAAAGAAGAAGCTTATGGG
CTTCCTTTCATCTTATCTGTCCATGAAGTACCACTGTGAGTTGCTAAACTACATTGATGTACCATTCATG

Alignment

ORF - retro_cjac_644 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.91 %
• Parental protein coverage: 67.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MSHLPMKLLRRKIEKRNLKLRQRNLKLQGASNLTLSETENGDVSEETMGGRKVKKSKHSMNVGFSDAQNG
          MSHL.MKLL..KI.K.NLKL.QRNLKL.G.SNLTLSETENG.VSEETMGGRK.KKSKHSMN.G.S.AQNG
Retrocopy MSHLLMKLLHKKIKKPNLKLQQRNLKLKGDSNLTLSETENGVVSEETMGGRKDKKSKHSMNLGLSEAQNG

Parental  DVSQEAVENIKVKKSPQKSIILTNGEGAMQSPNSVLKKKKKKKKRKMVNDAGPDTKK--AKAGNKGESED
          DVSQEAVE..KV.KS.QKS..LTNGE.AMQSPNS...KKKKKKKRKMVNDAGPDTKK..AK..NKGESE.
Retrocopy DVSQEAVEIFKVFKSLQKSAVLTNGEAAMQSPNSE-SKKKKKKKRKMVNDAGPDTKKKKAKTENKGESEE

Parental  ESAETPKETENNVEKPNNDEDDSEVPSLPLGLTGAFEDTSFASLSNLVNENTLKAIKEMG-FTNMTEIQH
          ..A.TPKETENNVEKP.NDEDDSEVPSLPL.LTGAFEDTSFASL.NLVNENTLKA.KE.G.FTNMT.IQH
Retrocopy QIA*TPKETENNVEKPDNDEDDSEVPSLPLELTGAFEDTSFASLCNLVNENTLKAVKETG<FTNMTKIQH

Parental  KSIRPLL-EGRDLLAAAKTGSGKTLAFLIPAVELIVKLKFMPRNGTGVLILSPTRELAMQ-TFGVLKELM
          KSIRPLL.E.RDLLAAA.TGSGKTLAFL.PA.E.I.KLK.MPRNGTGVLILSP.RELAMQ..FGVLKEL.
Retrocopy KSIRPLL<EDRDLLAAANTGSGKTLAFLVPAIEFI-KLKVMPRNGTGVLILSPARELAMQ<NFGVLKELI

Parental  THHVHTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEE
          TH.VHT.G.IMGGSNRSAE.QKL.NGINI.V.TPG.LLDHMQNTPGFM.KNLQCLVIDEAD.ILDVGFE.
Retrocopy THQVHT*GMIMGGSNRSAETQKLTNGINITVTTPGHLLDHMQNTPGFMHKNLQCLVIDEADCILDVGFED

Parental  ELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLK-KEPLYVGVDDDKANA-TVDGLEQGYVVCPS-EKR
          ELKQIIKLLPT.RQT.LFS.TQTRKVEDLARISL..KEP..V...DDK.N..TVDGLEQGY.VCP..EKR
Retrocopy ELKQIIKLLPTHRQTVLFSTTQTRKVEDLARISLQ<KEPI-VWCYDDKTNE<TVDGLEQGYIVCPL<EKR

Parental  FLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVL
          FLLLFTFLK.N.KKKLM.F.SS..S.KYH.ELLNYID.P..
Retrocopy FLLLFTFLKENQKKKLMGFLSSYLSMKYHCELLNYIDVPFM

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	0.02 RPM	26.60 RPM
SRP051959_heart	0.00 RPM	21.75 RPM
SRP051959_kidney	0.16 RPM	29.31 RPM
SRP051959_liver	0.00 RPM	28.90 RPM
SRP051959_lung	0.02 RPM	28.70 RPM
SRP051959_lymph_node	0.02 RPM	36.07 RPM
SRP051959_skeletal_muscle	0.00 RPM	24.92 RPM
SRP051959_spleen	0.00 RPM	31.93 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_644 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_644 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_644 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004950	2 retrocopies	retro_cfam_1404, retro_cfam_2116,
Choloepus hoffmanni	ENSCHOG00000004191	6 retrocopies	retro_chof_1221, retro_chof_1539, retro_chof_1636, retro_chof_2416, retro_chof_2418, retro_chof_721,
Callithrix jacchus	ENSCJAG00000021414	5 retrocopies	retro_cjac_2309, retro_cjac_2743, retro_cjac_4179, retro_cjac_644 , retro_cjac_753,
Echinops telfairi	ENSETEG00000017166	2 retrocopies	retro_etel_1919, retro_etel_297,
Microcebus murinus	ENSMICG00000017590	1 retrocopy	retro_mmur_1560,
Myotis lucifugus	ENSMLUG00000017607	1 retrocopy	retro_mluc_2279,
Monodelphis domestica	ENSMODG00000000533	1 retrocopy	retro_mdom_414,
Mus musculus	ENSMUSG00000001674	1 retrocopy	retro_mmus_2865,
Ochotona princeps	ENSOPRG00000001701	1 retrocopy	retro_opri_1039,