RetrogeneDB ID: retro_cjac_1912

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:56797542..56799004(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX21
• Ensembl ID: ENSCJAG00000012876
• Aliases: None
• Description: None

Sequence

>retro_cjac_1912
ATGTCAGGAAAACTCCATACTGACACTGGTTTGGAATCAGATACTGCAATGAAAAAAGTGGAGACACTGTGAAAGCAAGA
CGAGAAGAAAGAGAAAAAAGAGGAGCCAAAATCTAGTAGGACTGAAGAGACAGCAGAAGAGGAAGAAACTGTTTCCCCCA
AAGCTAAACAAGTTAAAAAGAGAGCAGAGCCTTCTGAAGTTGACATGAATTCTCCTAAATCCAAAAAGGCAAAAAAGAAA
GAGGAGCCATCTCAAGATGACATTTCTCCTAAAACCAAGAGTTTGAGAGAAATAAAAAGGAGCCCATTGTAAAGAAAGCG
GTTTCTTGTAAAACCAAACAAGTGATTAAAAAATGAGGAGCCTTCTGAGGAATAAACAGATGCTCCTAAGCCCAAGAAGA
TGAAGAAATAAATGGAAATTAATGGAAAAATCAGAGAGAAATCCAAACTGGAGAATGGATTTCCTCATTCTAAACCTGAC
TGTAACCCCAGTGAAGCTGCCAGTGAAGAAAGTAACAGTGAAATAGAGCAGGAAATACCCGTGGAACAAACAGAAGGCCA
TTTCTCTAATTTTCCCATATCTGAAGAAACTATTAAGCTTCTCAAAGGCCCAGGAGTGACCTTCCTATTTCTTATACAAG
CAAAGACATTCTGTCAAGTTCACAGCGGGAAGGACTTAACCGCACGGGTGCAGACAGGAACTGGGGAGACATTTTCCTTC
ACCATCCCTCTGACTGAGAAACTTCATGGGGAACTGCAGGGCAAGAAGAGAGGTGTCTCCCTCAGGGACTGGTTCTTGCA
CCTACAAGACAGCTGACAAATCAAGCAAGCAAAGACTTCAGTGACATCACAAAAAAGCTGTCAGTGGCTTGTTTTTATGT
GGAACTCCCTACGGAGGTCAATTTGAAGGCATGAGGAATGGGATTGATATCCTGGTTAGGACGCCAGGTCGTATCAAAGA
CCACATACAGAATGGAAACTAGATCTCACCAAACTGAAGCATGTTGTCCTGGATGAGGTTGACCAGATGCTGGATATGAG
ATTCGCTGATCAAGTGGAAGAGATTTTAAGTGTGGCCTATGACAAAGATTCTGAAGACAATCCCCAAACATTGCTTTTTT
CTGCAACTTGCCCTCATTGGTTATTTAATGTTGCCAAGAAATATATGAAATCTACATATGAACAGGGGGACCTGATTGGT
AAAAAGACTCAGAAGACGGCAATAACTGTGGACCCTCTGGCTACGAAGTGCCACTGGACTCAGGAGGGCAGCAATCATTG
GGGATGTCATCTGAATATACAGTGGTCATCAAGGGTGCACTGTCATCTTTTGTAAGACCAAGAAAGAAGCCTAGAAGCTG
TCCCAGAATTCAGCTATAAAGCAGGATGCCCAGTCATTGCATGGAGACATTGCACAGAAGCAAAGGAAAATCACCCTGAA
AAGTCTTAGAAATGGCCGCTTT

Alignment

ORF - retro_cjac_1912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.93 %
• Parental protein coverage: 62.32 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MPGKLRSDAALESVTAVKKVETLRKQTEKKEKKEKPKSNKIEEIAEEEETISPKAKKVKKKAEPSEVDMN
          M.GKL..D..LES.TA.KKVETL.KQ.EKKEKKE.PKS...EE.AEEEET.SPKAK.VKK.AEPSEVDMN
Retrocopy MSGKLHTDTGLESDTAMKKVETL*KQDEKKEKKEEPKSSRTEETAEEEETVSPKAKQVKKRAEPSEVDMN

Parental  SSKSNKAKKKEEPSQDDISPKTKSLRK-KKEP-IEKKAVSSKTKKVI-KNEEPSEEEIDAPKPKKMKKEK
          S.KS.KAKKKEEPSQDDISPKTKSLR..K..P.I.KKAVS.KTK.VI.KNEEPSEE..DAPKPKKMKK..
Retrocopy SPKSKKAKKKEEPSQDDISPKTKSLREIKRSP<IVKKAVSCKTKQVI>KNEEPSEE*TDAPKPKKMKK*M

Parental  EMNGETGEKSPKLKNGFPRSEPDCNPNEAASEESNSEMEQEIPVEQKEGAFSNFPISEETIKLLKGRGVT
          E.NG...EKS.KL.NGFP.S.PDCNP.EAASEESNSE.EQEIPVEQ.EG.FSNFPISEETIKLLKG.GVT
Retrocopy EINGKIREKS-KLENGFPHSKPDCNPSEAASEESNSEIEQEIPVEQTEGHFSNFPISEETIKLLKGPGVT

Parental  FLFPIQAKTFHHVYNGKDLIAQARTGTGKTFSFAIPLIEKLLGDLQDRKRGRP-PQVLVLAPTRELANQV
          FLF.IQAKTF..V..GKDL.A...TGTG.TFSF.IPL.EKL.G.LQ..KRG...PQ.LVLAPTR.L.NQ.
Retrocopy FLFLIQAKTFCQVHSGKDLTARVQTGTGETFSFTIPLTEKLHGELQGKKRGVS<PQGLVLAPTRQLTNQA

Parental  SKDFSDITKKLSVACFY-GGTPYGGQFERMRNGLISCVAIQEKVNHKIQNGLDL-LQKLPSSIPLPIGKP
          SKDFSDITKKLSVACFY..GTPYGGQFE.MRNG....V.........IQNG....L.KL...........
Retrocopy SKDFSDITKKLSVACFY<CGTPYGGQFEGMRNGIDILVRTPGRIKDHIQNGN*I<LTKLKHVVLDEVDQM

Parental  LSSNFVSSVPDLASAPLLKDSEDNPQTLLFSATCPHWVFNVAKKYMKSTYEQVDLIGKKTQKTAITVEHL
          L...F...V....S....KDSEDNPQTLLFSATCPHW.FNVAKKYMKSTYEQ.DLIGKKTQKTAITV..L
Retrocopy LDMRFADQVEEILSVAYDKDSEDNPQTLLFSATCPHWLFNVAKKYMKSTYEQGDLIGKKTQKTAITVDPL

Parental  AIQCHWTQ-RAAVIGDVIRVYSGHQGRTIIFCETKKEAQELSQNSAIKQDAQSLHGDIPQKQREITLKGF
          A..CHWTQ.RAA.IGDVI..YSGHQG.T.IFC.TKKEA..LSQNSAIKQDAQSLHGDI.QKQR.ITLK..
Retrocopy ATKCHWTQ>RAAIIGDVI*IYSGHQGCTVIFCKTKKEA*KLSQNSAIKQDAQSLHGDIAQKQRKITLKSL

Parental  RNGSF
          RNG.F
Retrocopy RNGRF

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	0.75 RPM	29.55 RPM
SRP051959_heart	0.67 RPM	23.26 RPM
SRP051959_kidney	0.89 RPM	27.60 RPM
SRP051959_liver	0.87 RPM	38.40 RPM
SRP051959_lung	0.98 RPM	36.03 RPM
SRP051959_lymph_node	1.19 RPM	50.96 RPM
SRP051959_skeletal_muscle	0.72 RPM	32.74 RPM
SRP051959_spleen	1.11 RPM	50.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1912 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1912 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1912 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013791	2 retrocopies	retro_cfam_1024, retro_cfam_1925,
Callithrix jacchus	ENSCJAG00000009966	2 retrocopies	retro_cjac_3639, retro_cjac_3640,
Callithrix jacchus	ENSCJAG00000012876	1 retrocopy	retro_cjac_1912 ,
Callithrix jacchus	ENSCJAG00000018844	1 retrocopy	retro_cjac_1298,
Macropus eugenii	ENSMEUG00000010586	1 retrocopy	retro_meug_1383,
Microcebus murinus	ENSMICG00000015112	1 retrocopy	retro_mmur_95,
Mus musculus	ENSMUSG00000020075	2 retrocopies	retro_mmus_582, retro_mmus_662,
Procavia capensis	ENSPCAG00000016697	1 retrocopy	retro_pcap_346,
Pongo abelii	ENSPPYG00000002389	1 retrocopy	retro_pabe_3816,
Tupaia belangeri	ENSTBEG00000002310	2 retrocopies	retro_tbel_1590, retro_tbel_4454,