RetrogeneDB ID: retro_cjac_2743

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:91874190..91875354(+)
• 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_2743
AAACTGGTGAATGATGCTGGGCCTGATACAAAAAAAGCAAAAACCAGAAACAAAGGGGAATCTGAAGATGAAAGTGCTGA
GATTCCTAAAGAAACAGAAAATAATGTGGAGAAGCCAAATAATGATGAAGATGACAGTGAGGTGCCCAGCCTGCCCCTGG
GACTGACAGGAGCTTTTGAGGATACTTCATTTGCTTCTCTATCTAATCTTGTCAATGAAAACACTCTGAAGGCAATAAAA
GAAATGGGTTTTACAAACATGACTGAAATTCAGCATAAAAGTATAAGACCACTTCTGGAAGGCAGGGATCTTCTAGCAGC
TGCAAAAACAGGAAGTGGTAAAACCCTAGCTTTTCTCATCCCTGCAGTTGAACACATTGTTAAGTTAAAGTTCATGCCCA
GGAATGGAACAGGAGTCCTTATTCTCTCACCTACTAGAGAACTAGCCATGCAAACTTTTGGTGTACTTAAGGAGCTAATG
ACTCACCACGTGCATACCTATGGGTTGATAATGGGTGGTAGTAACAGATCTGTGGAAGCACAGAATCTTGTTAATGGGAT
CAACATCATTGTGGCCACACCAGGCCGTCTGCTGGACCATATGCAGAATACCCCAGGGTTTATGTATAAGAACCTGCAGT
GTCTCGTTATTGATGAAGCTGATCGTATCTTGGATGTTGGGTTTGAAGAGGAATTAAAGCAAATTATTAAACTTTTGCCA
ACACGTAGACAGACTATGCTCTTTTCTGCCACCCAAACTTGAAAAGTTGAAGATCTGGCAAGGATTTCTCTGAAAAAGGA
GCCATTGTATGTTGGTGTTGATGATGATAAAGCTAATGCAACAGTGGATGGTCTTGAACAGGGGTATGTTGTTTGTCCTT
CTGAAAAGAGATTCCTTCTGCTCTTTACATTCCTTAAGAAGAACCGAAAGAAGAAACTTATGGTCTTCTTTTCATCTTGT
ATGTCCGTGAAATACCACTATGAGTTGCTGAATTACATTGATTTACCCGTCTTGGCCATTCATGGAAAGCAGAAGCAAAA
CAAGCATACAACCACATTCTTCCAGTTCTGCAATGCAGATTCAGGAACACTGTTGTGTACAGATGTGGCAACAAGAGGGC
TGGACATTCCCGAAGTCGACTGGATTGTTCAGTATGACCCCCCC

Alignment

ORF - retro_cjac_2743 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.16 %
• Parental protein coverage: 63.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMVNDAGPDTKKAKAGNKGESEDESAETPKETENNVEKPNNDEDDSEVPSLPLGLTGAFEDTSFASLSNL
          K.VNDAGPDTKKAK..NKGESEDESAE.PKETENNVEKPNNDEDDSEVPSLPLGLTGAFEDTSFASLSNL
Retrocopy KLVNDAGPDTKKAKTRNKGESEDESAEIPKETENNVEKPNNDEDDSEVPSLPLGLTGAFEDTSFASLSNL

Parental  VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLKFMPRNGTGVL
          VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVE.IVKLKFMPRNGTGVL
Retrocopy VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVEHIVKLKFMPRNGTGVL

Parental  ILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTPGFMYK
          ILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRS.EAQ.L.NGINIIVATPGRLLDHMQNTPGFMYK
Retrocopy ILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSVEAQNLVNGINIIVATPGRLLDHMQNTPGFMYK

Parental  NLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKANA
          NLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQT.KVEDLARISLKKEPLYVGVDDDKANA
Retrocopy NLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQT*KVEDLARISLKKEPLYVGVDDDKANA

Parental  TVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNKRT
          TVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNK.T
Retrocopy TVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNKHT

Parental  TTFFQFCNADSGTLLCTDVAARGLDIPEVDWIVQYDPP
          TTFFQFCNADSGTLLCTDVA.RGLDIPEVDWIVQYDPP
Retrocopy TTFFQFCNADSGTLLCTDVATRGLDIPEVDWIVQYDPP

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	0.11 RPM	26.60 RPM
SRP051959_heart	0.12 RPM	21.75 RPM
SRP051959_kidney	0.18 RPM	29.31 RPM
SRP051959_liver	0.26 RPM	28.90 RPM
SRP051959_lung	0.16 RPM	28.70 RPM
SRP051959_lymph_node	0.21 RPM	36.07 RPM
SRP051959_skeletal_muscle	0.02 RPM	24.92 RPM
SRP051959_spleen	0.06 RPM	31.93 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2743 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2743 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2743 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,