RetrogeneDB ID: retro_pabe_1786

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:28673318..28673861(+)
• Located in intron of: ENSPPYG00000010888

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_1786
ATGTTCAAGAAGTTTGATGAAAAGGAAAGTGTGTCCAACTGCATCCAGTTGAAAACGTCAGTTATTAAGGGCATTAAGAG
CCAACTGGTAGAGCAATTTCCAGGTATTGAACCATGGCTTAATCAAATCATGCCTAAGAAAGATCCTGTCAAAATAGTCC
GATGCCACGAACATACAGAAATCCTTACCGTAAGTGGGGAATTACTGTTTTTTAGACAAAGAAAGGGGCCTTTTTGTCCA
ACTCTAAGGTTGCTTCACAAATACCCTTTTATCCTGCCACACCAGCAGGTTGATAAAGGAGCTATCAAATTTGTACTCAG
CGGCGCAAATATTATGTGTCCAGGTTTAACTTCTCCTGGAGCTAAGCTGTACCCTGCTGCGGTAGATACGATTGTAGCAG
TCACGGCGGAAGGAAAACAGCATGCTCTGTGTGTTGGGGTCATGAAGATGTCTGCAGAAGATATTGAGAAAGTCAACAAA
GGAATCGGCATTGAAAACATCCATTATTTAAATGATGGGCTGTGGCACATGAAGACATATAAA

Alignment

ORF - retro_pabe_1786 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLF
          MFKKFDEKE.VSNCIQLKTSVIKGIK.QL.EQFPGIEPWLNQIMPKKDPVKIVRCHEH.EILTV.GELLF
Retrocopy MFKKFDEKESVSNCIQLKTSVIKGIKSQLVEQFPGIEPWLNQIMPKKDPVKIVRCHEHTEILTVSGELLF

Parental  FRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTVVAIMAEGKQ
          FRQR.GPF.PTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDT.VA..AEGKQ
Retrocopy FRQRKGPFCPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVAVTAEGKQ

Parental  HALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
          HALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
Retrocopy HALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK

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	0.17 RPM	8.68 RPM
SRP007412_cerebellum	0.97 RPM	6.32 RPM
SRP007412_heart	0.21 RPM	5.60 RPM
SRP007412_kidney	0.13 RPM	7.92 RPM
SRP007412_liver	0.31 RPM	11.35 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1786 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1786 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1786 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2422
Pan troglodytes	retro_ptro_1396
Gorilla gorilla	retro_ggor_1507
Macaca mulatta	retro_mmul_626
Mus musculus	retro_mmus_69
Rattus norvegicus	retro_rnor_1841

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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,