RetrogeneDB ID: retro_pabe_1833

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20_random:1586064..1586367(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCTS1
• Ensembl ID: ENSPPYG00000020687
• Aliases: None
• Description: malignant T cell amplified sequence 1 [Source:HGNC Symbol;Acc:23357]

Sequence

>retro_pabe_1833
ACTCTAAGGTTGCTTCACAAATACCCTTTTATCCTGCCACACCAGCAGGTTGATAAAGGAGCTATCAAATTTGTACTCAG
CGGCGCAAATATTATGTGTCCAGGTTTAACTTCTCCTGGAGTTAAGCTGTACCCTGCTGCGGTAGATACGATTGTAGCAG
TCACGGCGGAAGGAAAACAGCATGCTCTGTGTGTTGGGGTCATGAAGATGTCTGCAGAAGATATTGAGAAAGTCAACAAA
GGAATCGGCATTGAAAACATCCATTATTTAAATGATGGGCTGTGGCACATGAAGACATATAAA

Alignment

ORF - retro_pabe_1833 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.04 %
• Parental protein coverage: 55.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTVVAIMAEGKQHALCVGVMKM
          TLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPG.KLYPAAVDT.VA..AEGKQHALCVGVMKM
Retrocopy TLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGVKLYPAAVDTIVAVTAEGKQHALCVGVMKM

Parental  SAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
          SAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
Retrocopy SAEDIEKVNKGIGIENIHYLNDGLWHMKTYK

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.68 RPM
SRP007412_cerebellum	0.00 RPM	6.32 RPM
SRP007412_heart	0.00 RPM	5.60 RPM
SRP007412_kidney	0.00 RPM	7.92 RPM
SRP007412_liver	0.00 RPM	11.35 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1833 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1833 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1833 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034992	1 retrocopy	retro_btau_116,
Canis familiaris	ENSCAFG00000018545	1 retrocopy	retro_cfam_94,
Echinops telfairi	ENSETEG00000015462	1 retrocopy	retro_etel_19,
Felis catus	ENSFCAG00000008448	2 retrocopies	retro_fcat_1009, retro_fcat_310,
Myotis lucifugus	ENSMLUG00000015101	1 retrocopy	retro_mluc_16,
Mustela putorius furo	ENSMPUG00000001407	1 retrocopy	retro_mputfur_98,
Mus musculus	ENSMUSG00000000355	3 retrocopies	retro_mmus_2504, retro_mmus_2505, retro_mmus_69,
Oryctolagus cuniculus	ENSOCUG00000014315	1 retrocopy	retro_ocun_212,
Pongo abelii	ENSPPYG00000020687	2 retrocopies	retro_pabe_1786, retro_pabe_1833 ,
Ictidomys tridecemlineatus	ENSSTOG00000011496	2 retrocopies	retro_itri_1136, retro_itri_1468,