RetrogeneDB ID: retro_cjac_2306

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:302607..303255(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN6
• Ensembl ID: ENSCJAG00000004288
• Aliases: None
• Description: None

Sequence

>retro_cjac_2306
ATCACTGGCGTTATCCTTCTAGCAGTTGGCATTTGGGGCAAGGTGAGCCTGGAGAATTACTTTTCTCTTTTAAATGAGAA
GGCCACCAACGTCTCCTTCGTGCTCATTGGTACTGGTACCGTCATTGTTCTTTTGTGCACGTTTGGTTGTTTTGCTACCT
GCCGAGTTTCTGCATGGATGCTAAAATTGTATGCAATGTTTCTGACTCTCATTTTTTTGGTCGAACTGGTCGCTGCCATC
GTAGGATTTGTTTTCAGACATGAGATTAAGAACAGCTTTAAGAATAATTATGAGAAGGCTTTGAAGCAGTATAACTCTAC
AGGAGATTATAGAAGCAATGCAGTAGACAAGATCCAAAATACGTTGCATTGTTGTGGTGTCACCGATTATAGAGATTGGA
CAGATACTAATTATTACTCAGAAAAAGGATTTCCCAAGAGTTGCTGTAAACTTGAACATTGTACTCCACAGAGAGATGCA
AATAAAGTAAACAATGAAGGTTGTTTTATAAAGGTGATGACCATTATAGAGTCAGAAATGGGAGTCGTTGCAGGAATTTC
GTTTGGAGTTGCTTGCTTCCAGCTGATTGGAATCTTTCTCACCTACTGCCTCTCTCGTGCCATAACAAATAACCAGTAGG
AGATAGTG

Alignment

ORF - retro_cjac_2306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.77 %
• Parental protein coverage: 84.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ITGVILLAVGIWGKVSLENYFSLLNEKATNVPFVLIGTGTVIILLGTFGCFATCRVSAWMLKLYAMFLTL
          ITGVILLAVGIWGKVSLENYFSLLNEKATNV.FVLIGTGTVI.LL.TFGCFATCRVSAWMLKLYAMFLTL
Retrocopy ITGVILLAVGIWGKVSLENYFSLLNEKATNVSFVLIGTGTVIVLLCTFGCFATCRVSAWMLKLYAMFLTL

Parental  IFLVELVAAIVGFVFRHEIKNSFKNNYEKALKQYNSTGDYRSNAVDKIQNTSLHCCGVTDYRDWTDTNYY
          IFLVELVAAIVGFVFRHEIKNSFKNNYEKALKQYNSTGDYRSNAVDKIQNT.LHCCGVTDYRDWTDTNYY
Retrocopy IFLVELVAAIVGFVFRHEIKNSFKNNYEKALKQYNSTGDYRSNAVDKIQNT-LHCCGVTDYRDWTDTNYY

Parental  SEKGFPKTCCKLEHCTPQRDANKVNNEGCFIKVMTIIESEMGVVAGISFGVACFQLIGIFLAYCLSRAIT
          SEKGFPK.CCKLEHCTPQRDANKVNNEGCFIKVMTIIESEMGVVAGISFGVACFQLIGIFL.YCLSRAIT
Retrocopy SEKGFPKSCCKLEHCTPQRDANKVNNEGCFIKVMTIIESEMGVVAGISFGVACFQLIGIFLTYCLSRAIT

Parental  NNQYEIV
          NNQ.EIV
Retrocopy NNQ*EIV

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	9.43 RPM	9.52 RPM
SRP051959_heart	1.37 RPM	1.56 RPM
SRP051959_kidney	2.88 RPM	3.39 RPM
SRP051959_liver	2.84 RPM	3.88 RPM
SRP051959_lung	1.35 RPM	1.85 RPM
SRP051959_lymph_node	0.66 RPM	0.78 RPM
SRP051959_skeletal_muscle	0.28 RPM	0.44 RPM
SRP051959_spleen	0.88 RPM	1.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2306 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2306 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2306 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017521	3 retrocopies	retro_cfam_1600, retro_cfam_1609, retro_cfam_878,
Callithrix jacchus	ENSCJAG00000004288	1 retrocopy	retro_cjac_2306 ,
Callithrix jacchus	ENSCJAG00000007935	1 retrocopy	retro_cjac_4051,
Echinops telfairi	ENSETEG00000012276	1 retrocopy	retro_etel_1987,
Loxodonta africana	ENSLAFG00000027296	1 retrocopy	retro_lafr_994,
Microcebus murinus	ENSMICG00000011370	1 retrocopy	retro_mmur_447,
Nomascus leucogenys	ENSNLEG00000007505	1 retrocopy	retro_nleu_1186,
Otolemur garnettii	ENSOGAG00000004869	1 retrocopy	retro_ogar_2827,
Sarcophilus harrisii	ENSSHAG00000000274	1 retrocopy	retro_shar_515,
Sus scrofa	ENSSSCG00000012481	1 retrocopy	retro_sscr_84,