RetrogeneDB ID: retro_cjac_2309

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:10289078..10290220(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_cjac_2309
CAGAATCAAAAGAGAAAAATGCTGAATGATGCTGGGCCTGACACAAAAAAAGCAAAAACTGAAAACAAAGGGGATTCTGA
ATAAGAAAGTACCGAGACTCATAAAGAAACAGAAAATAATGTGTAGAAGCCAGATAATGATGGAGATGACAGTGAGGTGC
CCAGCCTGCCCCTGAAACCGACAGGAGCTTTTGAGGATATTTCATTTGCTTCTCTATGCCATCTTGTCAATGAAAAAAAC
GCTCTGAAGGCAATAAAAGAAATGGGTTTTACAAACATGACTGAAATTCAGCAGAAAACTCTAAGACTACTCTGGAAGGC
AGGGCTCTTCCAGCAGCTGCAAAAACAGGCTGTGGTAAAACCCTGGCTTTTCTCACCCCTGCAGTTGAACCCATTGTTAC
GTTAAAGTTCATGCCCAGGAACGGAAGGGGAGTCCTTATTCTCTCACCTAGTAGAGAATTAGCCATGCAAACTTCTGGTG
TTCTTAAGGAGCTAATGACTCAGCATGTGCATACTTATGGGTTGATAATGGGTGGTGGTAACAGATCTGCTGAAGAACAG
AAACTTGCTAATGGGATCAACATCATCCTGGCCACACCAGGCTGTCTGCTGGACCATATGCAGAACACCCCAGTGTTTAT
GTGTAAAAATCTGCAGTGCCTGGTTATTGATAAAGCTGGTCAGATCTTGGATGCTGGATTTGAAGAGGAATTAAAGCAAA
TTATTAAACTTTTGCCAACACGTAGATAGACTGTGCTCTTTTCTGCCACTCAAACTCGAACAGTTGAAGACCTGGCTAGG
ATTTCTCTGAAAAAGGAGCCATTGTACATTGCTATTGATGATGACAAAGCTAATGCAACAGTGGATGGTCTTGAGCAGGG
ATATGTTGTTCGTCCTTCTGAAAAGAGATTCCTTCTGTTCTTCACATTCCTTGAGAAGAACCAAAAGAAGGAGCTCATGG
TCTTCTTTTCATCTTGTATGTCTGTGAAATACCACTGTGAGTTGCTGAACTACATTGATTTGCCCGTCTTGGCCATTCAT
GGAAAGCAAAAGCAAAATAAGCATACAACCACATTCTTCCAGTTGTGCAACGCAGATTCAGGAACACTATTGTATACAGA
TGTGGCGGCAGGAGGACTGGAC

Alignment

ORF - retro_cjac_2309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.03 %
• Parental protein coverage: 62.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKKKRKMVNDAGPDTKKAKAGNKGESEDESAETPKETENNVEKPNNDEDDSEVPSLPLGLTGAFEDTSFA
          ...KRKM.NDAGPDTKKAK..NKG.SE.ES.ET.KETENNV.KP.ND.DDSEVPSLPL..TGAFED.SFA
Retrocopy QNQKRKMLNDAGPDTKKAKTENKGDSE*ESTETHKETENNV*KPDNDGDDSEVPSLPLKPTGAFEDISFA

Parental  SLSNLVNE-NTLKAIKEMGFTNMTEIQHKSIRPL-LEGRDLLAAAKTGSGKTLAFLIPAVELIVKLKFMP
          SL..LVNE.N.LKAIKEMGFTNMTEIQ.K..R.L.LEGR.L.AAAKTG.GKTLAFL.PAVE.IV.LKFMP
Retrocopy SLCHLVNEKNALKAIKEMGFTNMTEIQQKTLRLL<LEGRALPAAAKTGCGKTLAFLTPAVEPIVTLKFMP

Parental  RNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQN
          RNG.GVLILSP.RELAMQT.GVLKELMT.HVHTYGLIMGG.NRSAE.QKLANGINII.ATPG.LLDHMQN
Retrocopy RNGRGVLILSPSRELAMQTSGVLKELMTQHVHTYGLIMGGGNRSAEEQKLANGINIILATPGCLLDHMQN

Parental  TPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYVGV
          TP.FM.KNLQCLVID.A..ILD.GFEEELKQIIKLLPTRR.T.LFSATQTR.VEDLARISLKKEPLY...
Retrocopy TPVFMCKNLQCLVIDKAGQILDAGFEEELKQIIKLLPTRR*TVLFSATQTRTVEDLARISLKKEPLYIAI

Parental  DDDKANATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGK
          DDDKANATVDGLEQGYVV.PSEKRFLL.FTFL.KN.KK.LMVFFSSCMSVKYH.ELLNYIDLPVLAIHGK
Retrocopy DDDKANATVDGLEQGYVVRPSEKRFLLFFTFLEKNQKKELMVFFSSCMSVKYHCELLNYIDLPVLAIHGK

Parental  QKQNKRTTTFFQFCNADSGTLLCTDVAARGLD
          QKQNK.TTTFFQ.CNADSGTLL.TDVAA.GLD
Retrocopy QKQNKHTTTFFQLCNADSGTLLYTDVAAGGLD

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	0.07 RPM	29.31 RPM
SRP051959_liver	0.04 RPM	28.90 RPM
SRP051959_lung	0.11 RPM	28.70 RPM
SRP051959_lymph_node	0.05 RPM	36.07 RPM
SRP051959_skeletal_muscle	1.88 RPM	24.92 RPM
SRP051959_spleen	0.04 RPM	31.93 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2309 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2309 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2309 has 0 orthologous retrocopies within eutheria group .

---

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,