RetrogeneDB ID: retro_cjac_4179

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:65661256..65663171(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022449
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_4179
GGGGCCTCAAATCTGACCCTATCAGAAACTGAAAATGGAGATGTGTCTGAAGAAACAATGGGAGGTAGAAAGGTTAAAAA
AATCAAAACATTCTATGAATGTGGGCTTCTCAGAAGCTCAAAATGGAGATGTGTCTCAAGAAGCAGTGGAAAATATAAAA
GTTTAAAAATCTCCCCAGAAATCCATCGTCTTAACCAATGGAGAAGGAGCAATGCAGTCTCCCAATTCAGAATCGAAGAA
GAAAAAGAGAAAAGTGGTGAATGATGCTGGGCCTGACACAAAAAAAGCAAAAACTGGAAACCAAGGGGAATCTGAAGAAT
AAAGTGCCAAGACTCGTAAAGAAACAGAAAATAATGTGGAGAAGCCAGATAATGATGAAGATGACAGTGAGGGGCCCAGT
CTGCCCCTGGGACTGACAAGAGCTTTTGAGGATACTTCATTTGCTTCTCTATGTAATCTTGTCAATGAAAACACTCTGAA
GGCAAGAAAAGAAATGGGTTTTATAAACATGACTGAAATTCAGCATAAAAGTATCAGACCACTTCTGGAAGGCAGGAATC
TTCTAGCAGCTGCAAAAACAGGCAGTGGTAAAACCCTGGCTTTTCTCATCCCTGCAGTTGAACTCATTGTTAAGTTAAAG
TTCATGCCCAGGAGTGAAACGGGAGTCCTTATTCTCTCACCTACTAGAAAACTAGCCATGCAAACTTTTGGTGTTCTTAA
GGAGCTAATGACTCACCACGTGCATACCTATGGGTTGATAATGGGTGGCAGTAACAGATCTGCGGAAGCACAGAAACTTG
CTAATGGAATCAACATCATTGTGGCCACACCAGGCTGTCTGCTGGATCATATGCAGAATACCCCAGGGTTTATGTATAAG
AACCTGCAGTGTCTGGTTATTGATGAAGCTGATCGTATCTTGGATGTTGGGTTTGAAGGGGAATTAAAGCAAATTATTAA
ACTTTTGCCAACACGTAGACAGACTACGCTCTTTTCAGCCACCCAAATTCAAAAAGTTGAAGACCTGGCAAGGATTTCTC
TGAAAAAGAAGCCATTGTATGTTGGTGTTGATGATGATAAAGCTAATGCAACAGTGGATGGTCTTGAACAGGGATATGTT
GTTGGTCCTACTGAAAAGAGATTCCCTCTGCTTTTTACATTCCTTAAGAAGAACCGAAAGAAGAAATTTGTGGTCTTCTT
TTCATCTTCTATGTCCGTGAAATACCACTATGAGTTGCTGAATTACATTGATTTGCCCATCTTGGCCATTCATGGAAAGC
AAAAGCAAAACAAGCGTACAACCACATTCTTCCAGTTCTGCAATGCAGATTCAGGAACACTATTCTGTACAGATGTGGCA
GCAAGAGGACTGGACATTCCTGAAGCAGACTGGATTGTTCAGTATGACCCCCCTGATGACCCTAAGGAATATATTCATCG
TGTGGGTAGAACAGCCAGAGGCCTAAATGGGAGAGGGCCTGCCTTGCTCATTTTGCGTCCAGAAGAATTGGGTTTTCTTC
ACTATTTGAAACAATCCAAGGTTCCATTAAGTGAATTTGAGTTTTCCTGGTCTAAAATTTCTGACATTCAGTCCCAGCTT
GAGAAATTGATTGAAAAGAACTACTTTCTTCGTAAGTCAGCCCAGGAAGCATATAAGTTGTACATATGCGCCTATGATTC
CCATTCTCTGAAGCAGATCTTTAATGTTAATAACTTAAATTTGCCTCAGGTTGCTCTGTCATTTGGTTTCAAGGTGCCTC
CCTTTGTTGATTTGAACATCAACAGCAATGAAGGCAAGCAGAAAAAGCGAGGAGGCGGTGGCGGATTTGGCTACCAGAAA
ACCAAAAAAGTTGAAAAGTCCAAAATCTTTAAACATATTAGCAAGAAATCGCCCGACAGCAGGCAGTTCTCTCAC

Alignment

ORF - retro_cjac_4179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.07 %
• Parental protein coverage: 95.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GASNLTLSETENGDVSEETMGGRKVKK-SKHSMNVGFSDAQNGDVSQEAVENIKVKKSPQKSIILTNGEG
          GASNLTLSETENGDVSEETMGGRKVKK.SKHSMNVGFS.AQNGDVSQEAVENIKV.KSPQKSI.LTNGEG
Retrocopy GASNLTLSETENGDVSEETMGGRKVKK>SKHSMNVGFSEAQNGDVSQEAVENIKV*KSPQKSIVLTNGEG

Parental  AMQSPNSVLKKKKKKKKRKMVNDAGPDTKKAKAGNKGESEDESAETPKETENNVEKPNNDEDDSEVPSLP
          AMQSPNS......KKKKRK.VNDAGPDTKKAK.GN.GESE..SA.T.KETENNVEKP.NDEDDSE.PSLP
Retrocopy AMQSPNS----ESKKKKRKVVNDAGPDTKKAKTGNQGESEE*SAKTRKETENNVEKPDNDEDDSEGPSLP

Parental  LGLTGAFEDTSFASLSNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPA
          LGLT.AFEDTSFASL.NLVNENTLKA.KEMGF.NMTEIQHKSIRPLLEGR.LLAAAKTGSGKTLAFLIPA
Retrocopy LGLTRAFEDTSFASLCNLVNENTLKARKEMGFINMTEIQHKSIRPLLEGRNLLAAAKTGSGKTLAFLIPA

Parental  VELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANGINIIVA
          VELIVKLKFMPR..TGVLILSPTR.LAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANGINIIVA
Retrocopy VELIVKLKFMPRSETGVLILSPTRKLAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANGINIIVA

Parental  TPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARI
          TPG.LLDHMQNTPGFMYKNLQCLVIDEADRILDVGFE.ELKQIIKLLPTRRQT.LFSATQ..KVEDLARI
Retrocopy TPGCLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEGELKQIIKLLPTRRQTTLFSATQIQKVEDLARI

Parental  SLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNY
          SLKK.PLYVGVDDDKANATVDGLEQGYVV.P.EKRF.LLFTFLKKNRKKK..VFFSS.MSVKYHYELLNY
Retrocopy SLKKKPLYVGVDDDKANATVDGLEQGYVVGPTEKRFPLLFTFLKKNRKKKFVVFFSSSMSVKYHYELLNY

Parental  IDLPVLAIHGKQKQNKRTTTFFQFCNADSGTLLCTDVAARGLDIPEVDWIVQYDPPDDPKEYIHRVGRTA
          IDLP.LAIHGKQKQNKRTTTFFQFCNADSGTL.CTDVAARGLDIPE.DWIVQYDPPDDPKEYIHRVGRTA
Retrocopy IDLPILAIHGKQKQNKRTTTFFQFCNADSGTLFCTDVAARGLDIPEADWIVQYDPPDDPKEYIHRVGRTA

Parental  RGLNGRGHALLILRPEELGFLRYLKQSKVPLSEFDFSWSKISDIQSQLEKLIEKNYFLHKSAQEAYKSYI
          RGLNGRG.ALLILRPEELGFL.YLKQSKVPLSEF.FSWSKISDIQSQLEKLIEKNYFL.KSAQEAYK.YI
Retrocopy RGLNGRGPALLILRPEELGFLHYLKQSKVPLSEFEFSWSKISDIQSQLEKLIEKNYFLRKSAQEAYKLYI

Parental  RAYDSHSLKQIFNVNNLNLPQVALSFGFKVPPFVDLNVNSNEGKQRKRGGGGGFGYQKTKKVEKSKIFKH
          .AYDSHSLKQIFNVNNLNLPQVALSFGFKVPPFVDLN.NSNEGKQ.KRGGGGGFGYQKTKKVEKSKIFKH
Retrocopy CAYDSHSLKQIFNVNNLNLPQVALSFGFKVPPFVDLNINSNEGKQKKRGGGGGFGYQKTKKVEKSKIFKH

Parental  ISKKSSDSRQFSH
          ISKKS.DSRQFSH
Retrocopy ISKKSPDSRQFSH

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	1.00 RPM	26.60 RPM
SRP051959_heart	4.12 RPM	21.75 RPM
SRP051959_kidney	2.33 RPM	29.31 RPM
SRP051959_liver	1.23 RPM	28.90 RPM
SRP051959_lung	2.81 RPM	28.70 RPM
SRP051959_lymph_node	1.42 RPM	36.07 RPM
SRP051959_skeletal_muscle	1.09 RPM	24.92 RPM
SRP051959_spleen	2.63 RPM	31.93 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4179 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4179 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4179 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,