RetrogeneDB ID: retro_cjac_2011

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 20:25232224..25233302(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000008364
• Aliases: None
• Description: None

Sequence

>retro_cjac_2011
GCCCTTTGCTCCTCCCTCAGAATGAATGGAGACCAGAAATCAGATGTTTATGCCCAAGAAAAGCAGGATTTCATTCAGCA
CTTCTCCCAGATCGTTAGGATGCTGACTGAGGATGAGATGGGGCACCCAGAGACAGGAGATGCTACTGCCTGGCTCAAGG
AGGTCCTGGAGTACAACGCCATTGGAGGCAAGTATCACCGGGGTTTGACAGTGCTATCAGCATTCCGGGAGCTGGTGGAG
CCAAGGAAACAGGATGCTGATAGTCTCCAGTGGGCCCTGACTGTGGGCTGGTGTGTGGAACTGCTGCAAGCTTTCTTCCT
GGTGGCAGATGACATCATGGATTCATACCTCACCCGCCGGGGATGATCTGCTGGTATCAGAAGCCAGGCGTGGGTTTGGA
TGCCATCAGTGATGCTATCCTTCTGCAAGCATGTATCTACCACCCGCTGAAGCTCTACTGCCGGGTGCAGCCCTATTACC
TGAACCTGATCGAGCTCTTCCTGCAGAGTTCCTAACAGACTGAGATTGGGCAGACCCCGGACCTCATCACAGCCCCCCAG
GGCAATGTGGATCTTGGCAGATTCACTGAAAAGAGATACAAATCTATTGTCAAGTACAAGACAGCTTTCTACTCCTTTTA
CCTTCCTGTAGCTGCAGCCATGTACATGGCAGGAATTGATGGCGAGAAGGAGCAAGCCAATGCCAAGAAGATCCTGCTGG
AGATGGGAGAGTTCTTTCAGATTCAGGATGATTACCTTGACCTCTTTGGGGACCCCAGTGTGACTCGCAAAGTTGGCACT
GACATCCAGGACAACAAATGCAGTTGGCTGATGGTCCAGTGTCTGCAACGGTCCACTCTGGAACAGTGCCAGATCCTGAA
GGAAAATTACGGGCAGAAGGAGGCTGAGAAGGTGGCCCGGGTGGAGGCATTATATGAGAAGCTGGATCTGCCGGCCGTGT
TCTTGAAGTATGAGGAAGACAGTCAGAACCATATTATGGGTCTCACTGAACAGTACGCAGCGCCCCTGCCCCAGCTATCT
TTCTGGGGCTTGCACGCAAAATCTACAAGCAGAAAAAG

Alignment

ORF - retro_cjac_2011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.33 %
• Parental protein coverage: 85.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ALCSSLRMNGDQKSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPETGDAIARLKEVLEYNAIGGKYHRGLT
          ALCSSLRMNGDQKSDVYAQEKQDF.QHFSQIVR.LTEDEMGHPETGDA.A.LKEVLEYNAIGGKYHRGLT
Retrocopy ALCSSLRMNGDQKSDVYAQEKQDFIQHFSQIVRMLTEDEMGHPETGDATAWLKEVLEYNAIGGKYHRGLT

Parental  VLVAFRELAEPRKQDADSLQRALTVGWCVELLQAFFLVTDDIMDSSLTRRG-QICWYQKPGVGLDAINDA
          VL.AFREL.EPRKQDADSLQ.ALTVGWCVELLQAFFLV.DDIMDS.LTRRG..ICWYQKPGVGLDAI.DA
Retrocopy VLSAFRELVEPRKQDADSLQWALTVGWCVELLQAFFLVADDIMDSYLTRRG<MICWYQKPGVGLDAISDA

Parental  VLLEACVYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLITAPQDNVDLDRFTEKRYKSIVKYKTA
          .LL.AC.Y..LKLYCR.QPYYLNLIELFLQSS.QTEIGQT.DLITAPQ.NVDL.RFTEKRYKSIVKYKTA
Retrocopy ILLQACIYHPLKLYCRVQPYYLNLIELFLQSS*QTEIGQTPDLITAPQGNVDLGRFTEKRYKSIVKYKTA

Parental  FYSFYLPVAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKVGTDIQDNKCSWLVV
          FYSFYLPVAAAMYMAGIDGEKE.ANAKKILLEMGEFFQIQDDYLDLFGDPSVT.KVGTDIQDNKCSWL.V
Retrocopy FYSFYLPVAAAMYMAGIDGEKEQANAKKILLEMGEFFQIQDDYLDLFGDPSVTRKVGTDIQDNKCSWLMV

Parental  QCLQRSTPEQRQILKENYGQKEAEKVARVKALYEELDLPAVFSKYEEDSYNHIMALIEQYAAPLP-PAIF
          QCLQRST.EQ.QILKENYGQKEAEKVARV.ALYE.LDLPAVF.KYEEDS.NHIM.L.EQYAAPLP.PAIF
Retrocopy QCLQRSTLEQCQILKENYGQKEAEKVARVEALYEKLDLPAVFLKYEEDSQNHIMGLTEQYAAPLP<PAIF

Parental  LGLARKIYKRKK
          LGLARKIYK.KK
Retrocopy LGLARKIYKQKK

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	0.49 RPM	23.47 RPM
SRP051959_heart	1.84 RPM	5.24 RPM
SRP051959_kidney	1.13 RPM	7.57 RPM
SRP051959_liver	1.69 RPM	106.46 RPM
SRP051959_lung	1.48 RPM	8.85 RPM
SRP051959_lymph_node	0.27 RPM	11.07 RPM
SRP051959_skeletal_muscle	1.90 RPM	5.57 RPM
SRP051959_spleen	1.34 RPM	6.70 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2011 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2011 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2011 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030749	2 retrocopies	retro_cfam_1822, retro_cfam_1888,
Callithrix jacchus	ENSCJAG00000008364	11 retrocopies	retro_cjac_1066, retro_cjac_1217, retro_cjac_1395, retro_cjac_157, retro_cjac_2011 , retro_cjac_2081, retro_cjac_2161, retro_cjac_299, retro_cjac_4154, retro_cjac_44, retro_cjac_70,
Echinops telfairi	ENSETEG00000001154	6 retrocopies	retro_etel_1770, retro_etel_1818, retro_etel_2179, retro_etel_730, retro_etel_743, retro_etel_990,
Homo sapiens	ENSG00000160752	6 retrocopies	retro_hsap_1519, retro_hsap_1558, retro_hsap_1560, retro_hsap_3871, retro_hsap_3872, retro_hsap_502,
Microcebus murinus	ENSMICG00000007468	1 retrocopy	retro_mmur_1148,
Macaca mulatta	ENSMMUG00000023144	3 retrocopies	retro_mmul_1190, retro_mmul_2152, retro_mmul_565,
Mus musculus	ENSMUSG00000059743	5 retrocopies	retro_mmus_1028, retro_mmus_1552, retro_mmus_2802, retro_mmus_3625, retro_mmus_590,
Nomascus leucogenys	ENSNLEG00000012099	6 retrocopies	retro_nleu_1486, retro_nleu_1727, retro_nleu_2301, retro_nleu_2405, retro_nleu_2595, retro_nleu_2692,
Pongo abelii	ENSPPYG00000000747	3 retrocopies	retro_pabe_1290, retro_pabe_1329, retro_pabe_235,
Pan troglodytes	ENSPTRG00000001422	9 retrocopies	retro_ptro_1028, retro_ptro_1048, retro_ptro_1049, retro_ptro_2637, retro_ptro_2638, retro_ptro_2639, retro_ptro_2940, retro_ptro_2995, retro_ptro_377,
Rattus norvegicus	ENSRNOG00000043377	3 retrocopies	retro_rnor_1175, retro_rnor_153, retro_rnor_2897,
Ictidomys tridecemlineatus	ENSSTOG00000004475	1 retrocopy	retro_itri_488,
Tursiops truncatus	ENSTTRG00000013326	1 retrocopy	retro_ttru_689,