RetrogeneDB ID: retro_cjac_753

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:2107309..2108605(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033156
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_753
TGGCTTTTCTCGTCCCTGCAGTTGAACTCATTGTTAAGGTTCATGCCCACGGATAGAACGGGGTCCTTATTCTCTCACTT
GCCATGCAAACTTTTGGGGTTCTTAAGGGGCTAATGACTCACCATGTGCACACCTGAGGGTTGAGAACGGCTGGCAGTAA
TGGATCTGCCGAAGTACAGAGACTCGCTAAGGGGATCATTGTCACCGTGGTCACACCAGGCTGTTTGCTGGACCGTATGT
AGAACACCCTAGGGGTTGTGTAGAAAAACCTACAGTGTCTGGCTATTGATAAAGCCGATCATATCTCAGATGTTGGATTT
GAAGAGGAATTAAAGTAAGTTACTAAACTTTTGCAAACATGCAGACTGACTATGCTCTTCTCTGCCACCCAAACTCAAAA
AGCTGAAGACCTAGCAGACGTGTCTCTGAAAAAGGAGCCACTGTATGTTGGTGTTGATGATGGTGAAGCTAATGCAACAG
TGGATGGTCTGGAGCAGGGATATGCTGTTTGTCCCTCTGATAAGAGGTTCCTTGTGCCCTTTACATTCCTTAAGAAGAAT
CGGAAGAAGAAGCTTACGGTCTCCTTTTCATCTTGTATGTCCGTGAAATACCACTGTGAGTTGCTGAACTACATCGACTC
ACCTGTCTGGCCATGCATGGAAAGAAAAGCAAAGTAAGTGTACAACCACATTCTTCCATTTCTGCCACACAGTTTCAGGA
GCACCGTTGTGTACAGGTGGGGCAGCGAGAGGACTGGACATTCCTGAAGTCGACTGGATTGTCCAGCCTGACCCCCCCGA
TGACCCTCAGGAATATGTTCATTGTGTAAGCAGAACAGCCAGAGGTCTAAACGGGAGAGGGCATGCCTTGCTCATCTTGT
GCCCAGAAGAAACAGGGTTCCTTCGCTACTTGAAACAATCCAAGGTTCTATTAAGTGAATTTGACTTTTCGTCATCTAAA
ACTTCTGACATTCAGTCTCAGCTTGAGAAATTTATTGAAAAGAATTACTTTCTTTGTGGGTCAGTCCAGGAAGCATCAGT
CACCCGTACGAGCCTATGATTCCCGTTCTCTGAAACAGATCTTTAACGTGAAGAACTTACGTTCGACTCAAGTTGCTCTG
TCGTTTGGCTTCAAAGCGCCTCCTTTTGTTGATCTGAATGTCGACGGCAATGAAGCCAAGCGGAAAAAGTGAGGAGGTGG
TGGTGGATTTGCTACCAGAAAACCAATAAAGTTCAGAAGTCCAAAATCTTTAAACGCATTAGCAGGAAATCATCTAATAG
CAGACAGTTACCTCAC

Alignment

ORF - retro_cjac_753 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.78 %
• Parental protein coverage: 65.28 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  FLIPAVELIVKLKFMPRNGTG-VLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANG
          .L.....L...L.FMP...TG.VLILS....LAMQTFGVLK.LMTHHVHT.GL...GSN.SAE.Q.LA.G
Retrocopy WLFSSLQLNSLLRFMPTDRTG<VLILS----LAMQTFGVLKGLMTHHVHT*GLRTAGSNGSAEVQRLAKG

Parental  INIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKV
          I...V.TPG.LLD.M.NT.G...KNLQCL.ID.AD.I.DVGFEEELK...KLL.T.R.TMLFSATQT.K.
Retrocopy IIVTVVTPGCLLDRM*NTLGVV*KNLQCLAIDKADHISDVGFEEELK*VTKLLQTCRLTMLFSATQTQKA

Parental  EDLARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYH
          EDLA..SLKKEPLYVGVDD..ANATVDGLEQGY.VCPS.KRFL..FTFLKKNRKKKL.V.FSSCMSVKYH
Retrocopy EDLADVSLKKEPLYVGVDDGEANATVDGLEQGYAVCPSDKRFLVPFTFLKKNRKKKLTVSFSSCMSVKYH

Parental  YELLNYIDLPV-LAIHGK-QKQNKRTTTFFQFCNADSGTLLCTDVAARGLDIPEVDWIVQYDPPDDPKEY
          .ELLNYID.PV.LA.HGK..KQ.K.TTTFF.FC...SG..LCT..AARGLDIPEVDWIVQ.DPPDDP.EY
Retrocopy CELLNYIDSPV<LAMHGK<EKQSKCTTTFFHFCHTVSGAPLCTGGAARGLDIPEVDWIVQPDPPDDPQEY

Parental  IHRVGRTARGLNGRGHALLILRPEELGFLRYLKQSKVPLSEFDFSWSKISDIQSQLEK-LIEKNYFLHKS
          .H.V.RTARGLNGRGHALLIL.PEE.GFLRYLKQSKV.LSEFDFS.SK.SDIQSQLEK.L.....F....
Retrocopy VHCVSRTARGLNGRGHALLILCPEETGFLRYLKQSKVLLSEFDFSSSKTSDIQSQLEK>LLKRITFFVGQ

Parental  AQEAYKSYIRAYDSHSLKQIFNVNNLNLPQVALSFGFKVPPFVDLNVNSNEGKQRKRGGGGGFG-YQKTK
          ......S..RAYDS.SLKQIFNV.NL...QVALSFGFK.PPFVDLNV..NE.K..K.GGGGGF..YQKT.
Retrocopy SRK-HQSPVRAYDSRSLKQIFNVKNLRSTQVALSFGFKAPPFVDLNVDGNEAKRKK*GGGGGFA<YQKTN

Parental  KVEKSKIFKHISKKSSDSRQFSH
          KV.KSKIFK.IS.KSS.SRQ..H
Retrocopy KVQKSKIFKRISRKSSNSRQLPH

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	26.60 RPM
SRP051959_heart	0.00 RPM	21.75 RPM
SRP051959_kidney	0.00 RPM	29.31 RPM
SRP051959_liver	0.00 RPM	28.90 RPM
SRP051959_lung	0.00 RPM	28.70 RPM
SRP051959_lymph_node	0.00 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_753 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_753 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_753 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1579
Pan troglodytes	retro_ptro_1064
Gorilla gorilla	retro_ggor_1201
Pongo abelii	retro_pabe_1301

---

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,