RetrogeneDB ID: retro_cjac_2883

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:59241623..59242392(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZC3H15
• Ensembl ID: ENSCJAG00000005931
• Aliases: None
• Description: None

Sequence

>retro_cjac_2883
GTAGCACAGAGTGAAGCTGAAAAGAAATTGAAGAAGGATGACAAGAAGGAAGAATTGCAGGAGCTGAATGAACTGTTCAG
ACCTGTTGTTGCTGCTCAAAAATCAGTAAAGGTGCAGATCCCCAGTCTGCGGTGTGTGCATTCTTCAAGCAAGGACAGTG
CGCTAAAGGAGATAAGTGTACGTTCTCTCCGGACTTGACTCTGGAGAGAAAATGTGAAAAGCGAAGTGTTTACATTGATG
CAAGAGATGAAGAACTTGAAAAAAATACTGTGGATAATTGGGATGAGAAAAAGCTGGAAGAAGTAGTGAACAAGAAGCAC
GGCGAGGCGGAGAAGAAAAAACCAAAAGCTCAAATAGTGTGCAAGCATTTCCTTGAAGCTGTTGAAAACAACAAGTATGG
CTGGTTTGGGGTATGCCCTGGAGGGGTGATATTTGCATGTATCATCATGCACTTCCTCCTGGATCTGTGTTGAAAAAAGA
TAAAAAGGAAGAAGAGAAAGAAGATGAAATTTCATTAGAAGATCTAATTGAAAGAGAGCATTCTGCCCTAGGTCCAAAGG
TTACCAAAATCACTCTAGAATCTTTTCTTGCATGGAAGAAAAGGAAAAGACAAGAAAAGATTGATAAACTTGAACAAGAC
ATGGAAAGAAGGAAAGCTGACTTCAAAGCAGGGAAAGCACTAGCGATCAGTGGTCGTGAAGTGTTTGAATTTCGTCCTGA
ACTGGTCAATGATGATGATGAGGAAGCAGATGACACCCACTACACCCAG

Alignment

ORF - retro_cjac_2883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.28 %
• Parental protein coverage: 64.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAQSEAEKKLKKDDKKKELQELNELFKPVVAAQK-ISKGADPKSVVCAFFKQGQCTKGDKCKFSHDLTLE
          VAQSEAEKKLKKDDKK.ELQELNELF.PVVAAQK.ISKGADP.S.VCAFFKQGQC.KGDKC.FS.DLTLE
Retrocopy VAQSEAEKKLKKDDKKEELQELNELFRPVVAAQK<ISKGADPQSAVCAFFKQGQCAKGDKCTFSPDLTLE

Parental  RKCEKRSVYIDARDEELEKDTMDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCKHFLEAIENNKYGWFWVC
          RKCEKRSVYIDARDEELEK.T.DNWDEKKLEEVVNKKHGEAEKKKPK.QIVCKHFLEA.ENNKYGWF.VC
Retrocopy RKCEKRSVYIDARDEELEKNTVDNWDEKKLEEVVNKKHGEAEKKKPKAQIVCKHFLEAVENNKYGWFGVC

Parental  PGG-GDICMYRHALPPGFVLKKDKKKEEKEDEISLEDLIERERSALGPNVTKITLESFLAWKKRKRQEKI
          PGG.GDICMY.HALPPG.VLKKDKK.EEKEDEISLEDLIERE.SALGP.VTKITLESFLAWKKRKRQEKI
Retrocopy PGG<GDICMYHHALPPGSVLKKDKKEEEKEDEISLEDLIEREHSALGPKVTKITLESFLAWKKRKRQEKI

Parental  DKLEQDMERRKADFKAGKALVISGREVFEFRPELVNDDDEEADDTHYTQ
          DKLEQDMERRKADFKAGKAL.ISGREVFEFRPELVNDDDEEADDTHYTQ
Retrocopy DKLEQDMERRKADFKAGKALAISGREVFEFRPELVNDDDEEADDTHYTQ

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	20.86 RPM
SRP051959_heart	0.00 RPM	15.49 RPM
SRP051959_kidney	0.04 RPM	31.64 RPM
SRP051959_liver	0.02 RPM	25.08 RPM
SRP051959_lung	0.07 RPM	23.83 RPM
SRP051959_lymph_node	0.00 RPM	26.73 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.05 RPM
SRP051959_spleen	0.06 RPM	26.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2883 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2883 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021762	1 retrocopy	retro_btau_1223,
Choloepus hoffmanni	ENSCHOG00000011958	1 retrocopy	retro_chof_2120,
Callithrix jacchus	ENSCJAG00000005931	2 retrocopies	retro_cjac_2883 , retro_cjac_3986,
Cavia porcellus	ENSCPOG00000012965	2 retrocopies	retro_cpor_1294, retro_cpor_919,
Dipodomys ordii	ENSDORG00000011664	1 retrocopy	retro_dord_666,
Loxodonta africana	ENSLAFG00000001563	1 retrocopy	retro_lafr_941,
Monodelphis domestica	ENSMODG00000027565	5 retrocopies	retro_mdom_1230, retro_mdom_1321, retro_mdom_1744, retro_mdom_1942, retro_mdom_871,
Oryctolagus cuniculus	ENSOCUG00000011903	1 retrocopy	retro_ocun_886,
Otolemur garnettii	ENSOGAG00000002182	2 retrocopies	retro_ogar_1093, retro_ogar_611,
Ochotona princeps	ENSOPRG00000015790	2 retrocopies	retro_opri_169, retro_opri_609,
Pan troglodytes	ENSPTRG00000012717	1 retrocopy	retro_ptro_348,
Rattus norvegicus	ENSRNOG00000005256	4 retrocopies	retro_rnor_2628, retro_rnor_284, retro_rnor_662, retro_rnor_925,
Sorex araneus	ENSSARG00000012071	1 retrocopy	retro_sara_363,