RetrogeneDB ID: retro_cjac_521

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:43687147..43687672(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMBIM4
• Ensembl ID: ENSCJAG00000014558
• Aliases: None
• Description: transmembrane BAX inhibitor motif containing 4 [Source:HGNC Symbol;Acc:24257]

Sequence

>retro_cjac_521
GTCTACAGCATCCTTTCTCTGCAAGTCCTCTTAACTACAATGGCTTCAACGGTTTTTTAATACTTTGAGTCTATACGAAC
ATTTGTACATGACAATCCTGCCTTAATTTTGCTGTTTGCCCTCGGATCTCTGGGATTGATTTTTGCATTGAATTTTAACA
GACATAACTATCCCCTTAACCTGTACCTAGTTTTTGGATTTACGTTATTGGAAGCACTAACTGTGGCTGTTATTGTTACT
TTCTATGATGTACATATTATTCTGCAAGCTTACATATTGACTACTGGAGTATTTTTTGGTTTGACTATGTATATTCTGCA
AGCTAAGAAGGATTTCATCAAATTAGGGGCAGGGCTGTTTGCTTTTTTGTGGATTTTGTGCTTGTCAGGAGTCTTCAAGT
TATTTTTTTATAGTGAGACAGTGGAGCTGGTCTTAGCTGCTGCAGGAGCCCTTCTTTTCTGTGGATTCATCATCCATGAC
ACACACTCACTGATGCATAAACTGTCACCTGAAGAATACCTAATT

Alignment

ORF - retro_cjac_521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.57 %
• Parental protein coverage: 73.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VYSILSLQVLLTTMASTVFLYFESIRTFVHDSPALILLFALGSLGLIFALNLNRHKYPLNLYLLFGFTLL
          VYSILSLQVLLTTMASTVF.YFESIRTFVHD.PALILLFALGSLGLIFALN.NRH.YPLNLYL.FGFTLL
Retrocopy VYSILSLQVLLTTMASTVF*YFESIRTFVHDNPALILLFALGSLGLIFALNFNRHNYPLNLYLVFGFTLL

Parental  EALTVAVVVTFYDVHIILQAYILTTGVFFGLTMYTLQAKRDFSKLGAGLFAFLWILCLSGFFKLFFYSET
          EALTVAV.VTFYDVHIILQAYILTTGVFFGLTMY.LQAK.DF.KLGAGLFAFLWILCLSG.FKLFFYSET
Retrocopy EALTVAVIVTFYDVHIILQAYILTTGVFFGLTMYILQAKKDFIKLGAGLFAFLWILCLSGVFKLFFYSET

Parental  VELVLAAAGALLFCGFIIYDTHSLMHKLSPEEYIL
          VELVLAAAGALLFCGFII.DTHSLMHKLSPEEY..
Retrocopy VELVLAAAGALLFCGFIIHDTHSLMHKLSPEEYLI

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	20.86 RPM
SRP051959_heart	0.00 RPM	17.61 RPM
SRP051959_kidney	0.00 RPM	23.14 RPM
SRP051959_liver	0.00 RPM	21.44 RPM
SRP051959_lung	0.00 RPM	22.69 RPM
SRP051959_lymph_node	0.00 RPM	27.60 RPM
SRP051959_skeletal_muscle	0.00 RPM	13.63 RPM
SRP051959_spleen	0.00 RPM	23.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_521 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_521 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_521 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014558	1 retrocopy	retro_cjac_521 ,
Cavia porcellus	ENSCPOG00000007728	1 retrocopy	retro_cpor_441,
Tarsius syrichta	ENSTSYG00000010967	3 retrocopies	retro_tsyr_1322, retro_tsyr_1408, retro_tsyr_936,