RetrogeneDB ID: retro_cjac_2172

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:111810672..111811099(+)
• Located in intron of: ENSCJAG00000004791

Retrocopy information

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

Parental gene information

• Parental gene symbol: COTL1
• Ensembl ID: ENSCJAG00000004056
• Aliases: None
• Description: coactosin-like 1 (Dictyostelium) [Source:HGNC Symbol;Acc:18304]

Sequence

>retro_cjac_2172
ATCACCACCAAGATCCACAAAGAGGCTTGCCCAGCGGCGTACAACCTGGTGCGCGACGACAGCTCGGCCGTCATCTGGGT
TACTTCTAAATATAACGGCTCCACCATTGTCCCCAGCGAGCAGGGAGCGGAGTACCAGCACTTCATCCAGCAGTGCACAG
ATGACGTCCGGTTGTTTGCCTTCGTGAGCTTCACCACCGGGGATGCCATGAGCAAGAGGTCCAAGTTTGCCCTCATCCCG
TGGATCGGTGAGGACATCAGTGGGCTGCAGGGCTCCAAAACCGGGACAGACAAGACCCTGATCAAGTAAGTCATACAGAA
TTTTGCTAAGGAGTTTGTGATCAGTGATCGGTAGGAGCTGGAGGAAGATTTCATCAAGAGTAAGCTGAAGAAGGTGGGGG
GGAGCTAATTACGACACCCAGACACAG

Alignment

ORF - retro_cjac_2172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATKIDKEACRAAYNLVRDDGSAVIWVTFKYDGSTIVPGEQGAEYQHFIQQCTDDVRLFAFVRFTTGDAM
          ..TKI.KEAC.AAYNLVRDD.SAVIWVT.KY.GSTIVP.EQGAEYQHFIQQCTDDVRLFAFV.FTTGDAM
Retrocopy ITTKIHKEACPAAYNLVRDDSSAVIWVTSKYNGSTIVPSEQGAEYQHFIQQCTDDVRLFAFVSFTTGDAM

Parental  SKRSKFALITWIGEDVSGLQRAKTGTDKTLVKEVVQNFAKEFVISDRKELEEDFIKSELKKA-GGANYDA
          SKRSKFALI.WIGED.SGLQ..KTGTDKTL.K.V.QNFAKEFVISDR.ELEEDFIKS.LKK..GGANYD.
Retrocopy SKRSKFALIPWIGEDISGLQGSKTGTDKTLIK*VIQNFAKEFVISDR*ELEEDFIKSKLKKV>GGANYDT

Parental  QTE
          QT.
Retrocopy QTQ

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	0.18 RPM	16.62 RPM
SRP051959_heart	0.23 RPM	4.79 RPM
SRP051959_kidney	0.31 RPM	27.87 RPM
SRP051959_liver	0.19 RPM	8.40 RPM
SRP051959_lung	0.36 RPM	18.02 RPM
SRP051959_lymph_node	0.41 RPM	32.88 RPM
SRP051959_skeletal_muscle	0.09 RPM	1.29 RPM
SRP051959_spleen	0.29 RPM	28.34 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2172 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2172 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004056	4 retrocopies	retro_cjac_1182, retro_cjac_2171, retro_cjac_2172 , retro_cjac_530,
Macaca mulatta	ENSMMUG00000007039	1 retrocopy	retro_mmul_1249,