RetrogeneDB ID: retro_ptro_579

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:120986113..120987136(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAE1
• Ensembl ID: ENSPTRG00000011202
• Aliases: None
• Description: Pan troglodytes SUMO1 activating enzyme subunit 1 (SAE1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246619]

Sequence

>retro_ptro_579
ATGGTGGAGAAGGAGGAGGCTGGAGGCGGCATCAGCCAGGAGGAGGCAGGCGCAGTATGACCAGCAGATCTGCCTATGGG
GACTGGAGGCCCCGAAATGGCTGCGAGCCTCCCACGTGCTTCTTGTCGGCATGAAAGGACTCGGGGCTGAAATTGCCAAG
AATCTCATCCTGGCAGGAGTGAAAGAACTGACCATGCTGGATCACGAACAGATATCTCCAGAAGAACCCGGAGCTCAGTT
CTTGATTCGTATTGGGTCTGTTGGCCGAAATACGGCTGAAGCCTCTTTGGAGCGAGCTCAGAATCTTAACCCCAAGGTGG
ATGTGAAGTTGGACACTGAGGATATAGAGAAGAAACCAGAGTCATTTTTCACTCAATTTGATGCTGTGTGTTGACTTGCT
GCTCCAGGGATGTCATAGTTAAGGTTGCCCAGATCTGTCACAAAAATAGCATCAGGTTCTTTGCAGGAGATGTTTCTAGC
TACCATGGATACACATTTGCCAATCTAGGAGAGCATGAGTTTGTAGAGGAGAAAACTAAAGTTGCTAAAGTTAGCCAAGG
AGTAGAAGATGGGCCTGATACCAAGAGAGTAAAACTTGATTCTTCTGAGACAACGATGGTCAAGAAGAAGGTGGTCTTCT
GCCCCGTTGAAGAAGCGCTGGAGGTGGACTGGAGCAGTGAGAAAGCAAAGGCTGCTCTGAAGCGCACGACCTCCGACCAC
TTTCTCCTTCAAGTGCTCCTAAAGTTCCGCACAGATAAAGGAAGAGATCCCAGTTCTGATACACACGGGGAATATTCCGA
GTTGTTGCTCCAGATACGAAACGATGTGCTTGACTCACTGGGTATTATTCCCGACCCGCGCTTTATCACATACTTCTTCT
CCGAGATGGCCCCAGTGTGTGCGGTGGTTGGAGGGATTTTGGCACAGGAAATTGTGAAGGCCCTGTCTCAGCAGGACCCT
CCTCACAACTTCTTCTTCAATGGCATGAAGGGGAATGGGATTGTGGAGTGGCTTGGCCCCAAG

Alignment

ORF - retro_ptro_579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVEKEEAGGGISEEEA-AQYDRQIRLWGLEAQKRLRASRVLLVGLKGLGAEIAKNLILAGVKGLTMLDHE
          MVEKEEAGGGIS.EEA.AQYD.QI.LWGLEA.K.LRAS.VLLVG.KGLGAEIAKNLILAGVK.LTMLDHE
Retrocopy MVEKEEAGGGISQEEA>AQYDQQICLWGLEAPKWLRASHVLLVGMKGLGAEIAKNLILAGVKELTMLDHE

Parental  QVTPEDPGAQFLIRTGSVGRNRAEASLERAQNLNPMVDVKVDTEDIEKKPESFFTQFDAVC-LTCCSRDV
          Q..PE.PGAQFLIR.GSVGRN.AEASLERAQNLNP.VDVK.DTEDIEKKPESFFTQFDAVC.LTCCSRDV
Retrocopy QISPEEPGAQFLIRIGSVGRNTAEASLERAQNLNPKVDVKLDTEDIEKKPESFFTQFDAVC<LTCCSRDV

Parental  IVKVDQICHKNSIKFFTGDVFGYHGYTFANLGEHEFVEEKTKVAKVSQGVEDGPDTKRAKLDSSETTMVK
          IVKV.QICHKNSI.FF.GDV..YHGYTFANLGEHEFVEEKTKVAKVSQGVEDGPDTKR.KLDSSETTMVK
Retrocopy IVKVAQICHKNSIRFFAGDVSSYHGYTFANLGEHEFVEEKTKVAKVSQGVEDGPDTKRVKLDSSETTMVK

Parental  KKVVFCPVKEALEVDWSSEKAKAALKRTTSDYFLLQVLLKFRTDKGRDPSSDTYEEDSELLLQIRNDVLD
          KKVVFCPV.EALEVDWSSEKAKAALKRTTSD.FLLQVLLKFRTDKGRDPSSDT..E.SELLLQIRNDVLD
Retrocopy KKVVFCPVEEALEVDWSSEKAKAALKRTTSDHFLLQVLLKFRTDKGRDPSSDTHGEYSELLLQIRNDVLD

Parental  SLGISPDLLPEDFVRYCFSEMAPVCAVVGGILAQEIVKALSQRDPPHNNFFFFDGMKGNGIVECLGPK
          SLGI.PD.....F..Y.FSEMAPVCAVVGGILAQEIVKALSQ.DPPHN..FFF.GMKGNGIVE.LGPK
Retrocopy SLGIIPD---PRFITYFFSEMAPVCAVVGGILAQEIVKALSQQDPPHN--FFFNGMKGNGIVEWLGPK

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	0.02 RPM	125.25 RPM
SRP007412_cerebellum	0.00 RPM	85.82 RPM
SRP007412_heart	0.03 RPM	35.12 RPM
SRP007412_kidney	0.03 RPM	39.33 RPM
SRP007412_liver	0.03 RPM	44.91 RPM
SRP007412_testis	0.21 RPM	226.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_579 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_579 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_579 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_829
Gorilla gorilla	retro_ggor_679
Pongo abelii	retro_pabe_742
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 ,