RetrogeneDB ID: retro_pabe_2561

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:129166851..129167290(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TECR
• Ensembl ID: ENSPPYG00000009648
• Aliases: None
• Description: trans-2,3-enoyl-CoA reductase [Source:HGNC Symbol;Acc:4551]

Sequence

>retro_pabe_2561
ATGAAGCACTAAGAGGTGGAGATTCTGGACGCAAAGACAAGGGAGAAGCTGTGTTTCCTGGACAAGGGGGAGCCCCACAC
CACCAATGTGGAGATCAAGAACCTCTTCACCAAGACCCCTCTGTAGTGGTACCCTGCCCAGCAGTGCCTCCACCTGGACC
CCAAGGGCAAGTCCCTGAAGGATGAGGATGTTCTGCAAAAGCTGCCCGGGGCGCCACGGCCACACTCTACTTCCAGGGCC
TGGGGGCCAAGATCAGCTGGGTGACGGTCTTCCTAACAGAGTACGGGGGGCGTCTTTTCATCTACTTGCTCTTCTATGAG
TGCCCTTCATCTATGGCCACAAATATGACTTCACATCCAGTCGGGATTCGGTGGTGCACATCGCCTGCATCTGTCACTCA
TTCCACAATGTCAAGCACCTGCTGGAGACGCTCTTCATG

Alignment

ORF - retro_pabe_2561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.33 %
• Parental protein coverage: 56.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKHYEVEILDAKTREKLCFLDKVEPHATIAEIKNLFTKTHPQWYPARQSLRLDPKGKSLKDEDVLQKLPV
          MKH.EVEILDAKTREKLCFLDK.EPH.T..EIKNLFTKT...WYPA.Q.L.LDPKGKSLKDEDVLQKLP.
Retrocopy MKH*EVEILDAKTREKLCFLDKGEPHTTNVEIKNLFTKTPL*WYPAQQCLHLDPKGKSLKDEDVLQKLPG

Parental  -GTTATLYFRDLGAQISWVTVFLTEYAGPLFIYLLFYFR-VPFIYGHKYDFTSSRHTVVHLACICHSFHY
          .G.TATLYF..LGA.ISWVTVFLTEY.G.LFIY.L.....VPFIYGHKYDFTSSR..VVH.ACICHSFH.
Retrocopy <GATATLYFQGLGAKISWVTVFLTEYGGRLFIY-LLFYE<VPFIYGHKYDFTSSRDSVVHIACICHSFHN

Parental  VKRLLETLFV
          VK.LLETLF.
Retrocopy VKHLLETLFM

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	56.67 RPM
SRP007412_cerebellum	0.00 RPM	51.44 RPM
SRP007412_heart	0.00 RPM	9.66 RPM
SRP007412_kidney	0.00 RPM	41.93 RPM
SRP007412_liver	0.00 RPM	27.45 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2561 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2561 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2561 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000020013	1 retrocopy	retro_etel_1012,
Homo sapiens	ENSG00000099797	1 retrocopy	retro_hsap_3092,
Mus musculus	ENSMUSG00000031708	1 retrocopy	retro_mmus_1662,
Nomascus leucogenys	ENSNLEG00000013546	1 retrocopy	retro_nleu_124,
Pongo abelii	ENSPPYG00000009648	2 retrocopies	retro_pabe_2561 , retro_pabe_3591,
Rattus norvegicus	ENSRNOG00000021808	1 retrocopy	retro_rnor_579,