RetrogeneDB ID: retro_pabe_742

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:119976485..119977589(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAE1
• Ensembl ID: ENSPPYG00000010168
• Aliases: SAE1, UBLE1A
• Description: SUMO-activating enzyme subunit 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5NVN7]

Sequence

>retro_pabe_742
GTTGGTGGTGCGCAGGGCCGGCGGGCAGTTGGCATGAGCAGGACCGGAGCTGAGGCAGGAAAAGCCGGCACTTTGGTGGA
GAAGGAGGAGGCTGGAGGCAGCATCAGCGAGGAGGAGGCGGGCGCAGTATGACCGGCAGATCTGCCTGTGGGGACTGGAG
GCCCAGAAATATCTGCGGGCCTCCCAGTTGCTTCTTGTCGGCATGAAAGGACTCGGGGCTGAAATTGCCAAGAATCTTAT
CCTGGCAGGAGTGAAAGGACTGACCATGCTGGATCACGAACAGGTATCTCCAGAAGAACCCAGAGCTCTGTTCTTGATTC
GTATTGGGTCTGTTGGCCGAAATAGGGCTGAAGCCTCTTTGGAGCAAGCTCAGAATCTTAACCCCATGGTGGATGTGAAG
GTGGACACTGAGGATATAGAGAAGAAACCAGAGTCATTTTTCACTCAATTTGATGCTGTGTGTTGACTTGCTGCTCCAGG
GATGTCATAGTTAAGGTTGACCAGATCTATCACAAAAATAGCATCAAGTTCTTTACAGGAGATGTAAAGAACCATGGATA
CACATTTGCCAATCTAGGAGAGCATGAGTTTGTGGAGGAGAAAACTAAAGTTGCCAAAGTTAGCCAAGGAGTAGAAGATG
GGCCTGATACCAAGAGAGTAAAATTTGATTCTTCTGAGACAACGATGGTCAAAAAGAAGGTGGTCTTCTGCCCCGTTAAA
GAAGCCCTGGAGGTGGACTGGAGCAGTGAGAAAGCAAAGGCTGCTCTGAAGTGCACGACCTCCGACCACTTTCTCCTTCA
AGCGCTCCTAAAGTTCCGCACAGATAAAGGAAGAGATCCCAGTTCTGATACACATGGGGAAGATTCCAAGCTGTTGCTCC
AGATACGAAACGATGTGCTTAACTCACTGCGCATTAGTCCTGACCTGCTTCCTGAGGACTTTATCACGTACTGCTTCTCC
GAGATGGCCCCAGTGTGTGCGGTGGTTGGAGGGATTTTGGCACAGGAAATTGTGAAGGCCCTGTCTCAGCAGGACCCTCC
TCACAACTTCTTCTTCTTCAATGGCATGAAGGGGAATGGGATTGTGGAGCGGCTTGGCCCCAAG

Alignment

ORF - retro_pabe_742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.71 %
• Parental protein coverage: 96.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VGGARVRRAVGLSGYGAEAGRAGAMVEKEEAGGGISEEEA-AQYDRQIRLWGLEAQKRLRASRVLLVGLK
          VGGA..RRAVG.S..GAEAG.AG..VEKEEAGG.ISEEEA.AQYDRQI.LWGLEAQK.LRAS..LLVG.K
Retrocopy VGGAQGRRAVGMSRTGAEAGKAGTLVEKEEAGGSISEEEA>AQYDRQICLWGLEAQKYLRASQLLLVGMK

Parental  GLGAEIAKNLILAGVKGLTMLDHEQVTPEDPGAQFLIRTGSVGRNRAEASLERAQNLNPMVDVKVDTEDI
          GLGAEIAKNLILAGVKGLTMLDHEQV.PE.P.A.FLIR.GSVGRNRAEASLE.AQNLNPMVDVKVDTEDI
Retrocopy GLGAEIAKNLILAGVKGLTMLDHEQVSPEEPRALFLIRIGSVGRNRAEASLEQAQNLNPMVDVKVDTEDI

Parental  EKKPESFFTQFDAVC-LTCCSRDVIVKVDQICHKNSIKFFTGDVFGYHGYTFANLGEHEFVEEKTKVAKV
          EKKPESFFTQFDAVC.LTCCSRDVIVKVDQI.HKNSIKFFTGDV...HGYTFANLGEHEFVEEKTKVAKV
Retrocopy EKKPESFFTQFDAVC<LTCCSRDVIVKVDQIYHKNSIKFFTGDVKN-HGYTFANLGEHEFVEEKTKVAKV

Parental  SQGVEDGPDTKRAKLDSSETTMVKKKVVFCPVKEALEVDWSSEKAKAALKRTTSDYFLLQVLLKFRTDKG
          SQGVEDGPDTKR.K.DSSETTMVKKKVVFCPVKEALEVDWSSEKAKAALK.TTSD.FLLQ.LLKFRTDKG
Retrocopy SQGVEDGPDTKRVKFDSSETTMVKKKVVFCPVKEALEVDWSSEKAKAALKCTTSDHFLLQALLKFRTDKG

Parental  RDPSSDTYEEDSELLLQIRNDVLDSLGISPDLLPEDFVRYCFSEMAPVCAVVGGILAQEIVKALSQRDPP
          RDPSSDT..EDS.LLLQIRNDVL.SL.ISPDLLPEDF..YCFSEMAPVCAVVGGILAQEIVKALSQ.DPP
Retrocopy RDPSSDTHGEDSKLLLQIRNDVLNSLRISPDLLPEDFITYCFSEMAPVCAVVGGILAQEIVKALSQQDPP

Parental  HNNFFFFDGMKGNGIVECLGPK
          H.NFFFF.GMKGNGIVE.LGPK
Retrocopy H-NFFFFNGMKGNGIVERLGPK

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	185.00 RPM
SRP007412_cerebellum	0.00 RPM	52.77 RPM
SRP007412_heart	0.00 RPM	25.08 RPM
SRP007412_kidney	0.00 RPM	30.86 RPM
SRP007412_liver	0.09 RPM	21.82 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_742 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_742 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_742 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_829
Pan troglodytes	retro_ptro_579
Gorilla gorilla	retro_ggor_679
Macaca mulatta	retro_mmul_1087

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004180	1 retrocopy	retro_cfam_1705,
Dipodomys ordii	ENSDORG00000012199	1 retrocopy	retro_dord_638,
Homo sapiens	ENSG00000142230	1 retrocopy	retro_hsap_829,
Gorilla gorilla	ENSGGOG00000013078	1 retrocopy	retro_ggor_679,
Macaca mulatta	ENSMMUG00000009506	1 retrocopy	retro_mmul_1087,
Nomascus leucogenys	ENSNLEG00000002965	1 retrocopy	retro_nleu_261,
Nomascus leucogenys	ENSNLEG00000002966	1 retrocopy	retro_nleu_262,
Pongo abelii	ENSPPYG00000010168	1 retrocopy	retro_pabe_742 ,
Pan troglodytes	ENSPTRG00000011202	1 retrocopy	retro_ptro_579,