RetrogeneDB ID: retro_cjac_2796

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:29901029..29901715(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000015165
• Aliases: None
• Description: None

Sequence

>retro_cjac_2796
CATTCAAACTCCTCCCTGTGACACACTGAAACAGTGACGGCACAGCAGAAAGAATGGAAGATGTTTATAGGAGGACTTAG
CCAGGACACTATAAAGAAAGATCTGAAGGACTGCTTTTCCAAATTTGGTGAAGTTGTAGACTGCAGTCTGAAGTTAGATC
CTATCACAGGGCGATCAAAGGGGTTTGGCTTTGTGCTATTTAAAGAATCGGAGAGTGTAGATAAGGTTATGGATCAGAAA
GAACATAAATTGAATGGGAAGGTTCTTACCCTGTTCAATCCTAAAAGGGCCAAAGTCATGAAAACAAAAGAGCCGGTTAA
AAATTTTTTGTTGGTGGCCTTTCTCCAGATACACCTGAAGAGAACATAAGGGAGTACTTTGGTGGTTTTGGTGAGGTGGA
ATCCGTAGAGCTCCTCATGGACAACAAGACCAATAAGAGGTGTGGCTTCTGCTTCATTACCTCTAAGGAAGAACCAGTGA
AGAAAATGAAGAAGAAATATCAAAGTGTTGGTCTTAGAAAATGTGAAATAAAAGTAGCCATGTCGAAGGAACAGTATCAT
CAACAGCAACAGTGGGAATCTAGAGGAGGTTTTGCAGGAAGAGCTCGTGGAAGAGGTGGTGACCAGCAGAGTGGTTATGG
GAAGGTATCCAGGCGATGTGGTCATCAAAATAGCTACAAACCATAC

Alignment

ORF - retro_cjac_2796 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.78 %
• Parental protein coverage: 78.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HSNSSPRHTEAATAQREEWKMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKES
          HSNSS..HTE..TAQ..EWKMFIGGLS.DT.KKDLKD.FSKFGEVVDC.LKLDPITGRS.GFGFVLFKES
Retrocopy HSNSSL*HTETVTAQQKEWKMFIGGLSQDTIKKDLKDCFSKFGEVVDCSLKLDPITGRSKGFGFVLFKES

Parental  ESVDKVMDQKEHKLNGKVI---DPKRAKAMKTKEPVK-KIFVGGLSPDTPEEKIREYFGGFGEVESIELP
          ESVDKVMDQKEHKLNGKV.....PKRAK.MKTKEPVK.K.FVGGLSPDTPEE.IREYFGGFGEVES.EL.
Retrocopy ESVDKVMDQKEHKLNGKVLTLFNPKRAKVMKTKEPVK<KFFVGGLSPDTPEENIREYFGGFGEVESVELL

Parental  MDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVAMSKEQYQQQQQWGSRGGFAGRARGRGG
          MDNKTNKR.GFCFIT.K.EEPVKK.M.KKY..VGL.KCEIKVAMSKEQY.QQQQW.SRGGFAGRARGRGG
Retrocopy MDNKTNKRCGFCFITSK-EEPVKK-MKKKYQSVGLRKCEIKVAMSKEQYHQQQQWESRGGFAGRARGRGG

Parental  DQQSGYGKVSRRGGHQNSYKPY
          DQQSGYGKVSRR.GHQNSYKPY
Retrocopy DQQSGYGKVSRRCGHQNSYKPY

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	19.59 RPM
SRP051959_heart	0.00 RPM	19.68 RPM
SRP051959_kidney	0.02 RPM	23.10 RPM
SRP051959_liver	0.00 RPM	12.76 RPM
SRP051959_lung	0.00 RPM	30.18 RPM
SRP051959_lymph_node	0.02 RPM	34.18 RPM
SRP051959_skeletal_muscle	0.00 RPM	13.17 RPM
SRP051959_spleen	0.00 RPM	31.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2796 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2796 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2796 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007908	2 retrocopies	retro_cjac_2285, retro_cjac_3041,
Callithrix jacchus	ENSCJAG00000015165	1 retrocopy	retro_cjac_2796 ,
Callithrix jacchus	ENSCJAG00000015197	1 retrocopy	retro_cjac_2589,
Dipodomys ordii	ENSDORG00000012507	1 retrocopy	retro_dord_649,
Homo sapiens	ENSG00000138668	1 retrocopy	retro_hsap_4689,
Gorilla gorilla	ENSGGOG00000026760	1 retrocopy	retro_ggor_2916,
Loxodonta africana	ENSLAFG00000016483	1 retrocopy	retro_lafr_686,
Pan troglodytes	ENSPTRG00000016215	1 retrocopy	retro_ptro_3116,
Sarcophilus harrisii	ENSSHAG00000013312	1 retrocopy	retro_shar_752,
Tupaia belangeri	ENSTBEG00000002327	1 retrocopy	retro_tbel_2698,
Tarsius syrichta	ENSTSYG00000010395	3 retrocopies	retro_tsyr_1092, retro_tsyr_2070, retro_tsyr_269,
Tursiops truncatus	ENSTTRG00000007592	1 retrocopy	retro_ttru_1913,
Vicugna pacos	ENSVPAG00000004374	2 retrocopies	retro_vpac_484, retro_vpac_97,