RetrogeneDB ID: retro_cjac_723

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:96116380..96116980(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAGLN
• Ensembl ID: ENSCJAG00000012755
• Aliases: LOC100385619, TAGLN, transgelin
• Description: transgelin [Source:HGNC Symbol;Acc:11553]

Sequence

>retro_cjac_723
ATGGCCAACAAGGGTCCTTCCTATGGCATGAGCCTCAAAGCGCAGTCCAAAATTGAGAATAACTACGACGAGGAGCCAGA
GGAGCAGCTGGTGGAGTGGATCATAGTGCAGCGTGGCCTTGATGTGGGCCGCCCAGACCATGGGCGCCTGGGCTTCCAGG
TTTGGCTAAAGAATGGCGTGATTCTGAGCAAGCTGGTGAATAGCCTGTACCCTGATGGCTCCAAGTCTGTGAAGGTGCCT
GAGAATCTGCCCTCCAGGATCTTCAAGCAGATGGAACAGGTGGCCCAGTTCCTGAAGGCAGCTGAGAGCTATGGGGTCAC
CAAGACTAACATGTTCCAGACTGTTGATCTCTTTGAAGGCAAAGACATGGCAGCAGTGCAGAAGACCCTGAAGGCTTTGG
GCAGCTTGGTAGTAACCAAGAATGATGGACACTACTGTGGAGATCCCAATTGATTTATGAAGAAAGCACAGGAGCATAAG
AGATAATTCACAGAGAGCCAGCTGCAGGAGGGAAAGTATGTCATTGGCCTTCAGATGGGCAGCAACAGAGGGGCCTCCCA
GGCAGGCATGACAGGCTACGGACAACCTTGGCAGAACATC

Alignment

ORF - retro_cjac_723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87. %
• Parental protein coverage: 99.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MANKGPSYGMSREVQSKIEKKYDEELEERLVEWIIVQCGPDVGRPDRGRLGFQVWLKNGVILSKLVNSLY
          MANKGPSYGMS...QSKIE..YDEE.EE.LVEWIIVQ.G.DVGRPD.GRLGFQVWLKNGVILSKLVNSLY
Retrocopy MANKGPSYGMSLKAQSKIENNYDEEPEEQLVEWIIVQRGLDVGRPDHGRLGFQVWLKNGVILSKLVNSLY

Parental  PDGSKPVKVPENPPSMVFKQMEQVAQFLKAAEDYGVTKTDMFQTVDLFEGKDMAAVQRTLMALGSLAVTK
          PDGSK.VKVPEN.PS..FKQMEQVAQFLKAAE.YGVTKT.MFQTVDLFEGKDMAAVQ.TL.ALGSL.VTK
Retrocopy PDGSKSVKVPENLPSRIFKQMEQVAQFLKAAESYGVTKTNMFQTVDLFEGKDMAAVQKTLKALGSLVVTK

Parental  NDGHYRGDPNWFMKKAQEHKREFTESQLQEGKHVIGLQMGSNRGASQAGMTGYGRPRQII
          NDGHY.GDPN.FMKKAQEHKR.FTESQLQEGK.VIGLQMGSNRGASQAGMTGYG.P.Q.I
Retrocopy NDGHYCGDPN*FMKKAQEHKR*FTESQLQEGKYVIGLQMGSNRGASQAGMTGYGQPWQNI

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	0.07 RPM	207.63 RPM
SRP051959_heart	0.00 RPM	344.51 RPM
SRP051959_kidney	0.00 RPM	30.53 RPM
SRP051959_liver	0.00 RPM	5.65 RPM
SRP051959_lung	0.00 RPM	44.44 RPM
SRP051959_lymph_node	0.09 RPM	22.15 RPM
SRP051959_skeletal_muscle	0.00 RPM	24.79 RPM
SRP051959_spleen	0.06 RPM	29.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_723 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_723 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_723 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005530	1 retrocopy	retro_cjac_681,
Callithrix jacchus	ENSCJAG00000006156	2 retrocopies	retro_cjac_2035, retro_cjac_2444,
Callithrix jacchus	ENSCJAG00000012755	2 retrocopies	retro_cjac_723 , retro_cjac_778,
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Microcebus murinus	ENSMICG00000002371	1 retrocopy	retro_mmur_666,
Oryctolagus cuniculus	ENSOCUG00000011970	1 retrocopy	retro_ocun_116,