RetrogeneDB ID: retro_pabe_3335

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:58269082..58270015(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT10
• Ensembl ID: ENSPPYG00000012144
• Aliases: None
• Description: septin-10 [Source:RefSeq peptide;Acc:NP_001127203]

Sequence

>retro_pabe_3335
AATGTTAAACTTAAACATCAGACATAAGAACTCCAGGAAAGTAATGTTCGACTGAAATTGACCATTGTGAATAGAGTGGA
ATTTGGTGACCAAATAAATAAAGAAGAGAGCTACCAACTGATAGTTGACTACATAGATGCTCAGTTTGAGGCCTATCTCC
AAGAATAACTGAAGATTAAACGTTCTCTCTTTACCTACCATGATTCTCGCATCCATGTGTACCTCTACTTCATTTCACCC
ACAGGCCACTCTCTGAAGACACTTGATCTCTTAACCATGAAGAACCTTGACAGCAAGGTAAACATTATACCAGTGATTGC
CAATCACTGGTTTGTAAATACGGTTTCTAAAACTGAATTACAGAAGTTTAAGATCAAGTTCATGAGTGAATTGGTCAGCA
ATGGCGTCCAGATACACCAGTTTCCAACGGATGATGACACTATTGCTTAGGTCAATGCTGCAATGAATGGACAGTTGCCG
TTTGCTGCTGTGGGAAGTAAGGATGAGGTTAAAATCGGAAACAAGATGGTCAAAGCTCGCCAGTACCCTTGGGGTGTTGT
ACAAGTGGAAAATGAAAACCACTGTGACTTTGTAAAGCTGCGGGAAATGCTCATTTGTACAAATATGGAGGACCTGCGAG
AGCAGACCCATACCAGGCACTATGAGCTTTACAGGCGCTGCAAACTGGAGGAAATGGGCTTTACAGATGTGGGCCCAGAA
AACAAGCCGGTCAGTCTTCAAGAGACCTATGAAGCCAAAAGACATGACTTCCATGGTGAACGTCAGAGGAAGGAAGAAGA
AATGAAACAGATGTTTGTGCAGCCAGTAAAGGAGAAAGAAGCCATATTGAAAGAAGCTGAGAGAGAGCTACAGGCCAACT
TTGAGCACCTTAAGAGACTTCACCAAGAAGAGAGAATGAAGCTTGAAGAGAAG

Alignment

ORF - retro_pabe_3335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.6 %
• Parental protein coverage: 74.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVKLKAQTYELQESNVQLKLTIVNTVGFGDQINKEESYQPIVDYIDAQFEAYLQEELKIKRSLFTYHDSR
          NVKLK.QT.ELQESNV.LKLTIVN.V.FGDQINKEESYQ.IVDYIDAQFEAYLQE.LKIKRSLFTYHDSR
Retrocopy NVKLKHQT*ELQESNVRLKLTIVNRVEFGDQINKEESYQLIVDYIDAQFEAYLQE*LKIKRSLFTYHDSR

Parental  IHVCLYFISPTGHSLKTLDLLTMKNLDSKVNIIPVIAK---ADTVSKTELQKFKIKLMSELVSNGVQIYQ
          IHV.LYFISPTGHSLKTLDLLTMKNLDSKVNIIPVIA......TVSKTELQKFKIK.MSELVSNGVQI.Q
Retrocopy IHVYLYFISPTGHSLKTLDLLTMKNLDSKVNIIPVIANHWFVNTVSKTELQKFKIKFMSELVSNGVQIHQ

Parental  FPTDDDTIAKVNAAMNGQLPFAVVGSMDEVKVGNKMVKARQYPWGVVQVENENHCDFVKLREMLICTNME
          FPTDDDTIA.VNAAMNGQLPFA.VGS.DEVK.GNKMVKARQYPWGVVQVENENHCDFVKLREMLICTNME
Retrocopy FPTDDDTIA*VNAAMNGQLPFAAVGSKDEVKIGNKMVKARQYPWGVVQVENENHCDFVKLREMLICTNME

Parental  DLREQTHTRHYELYRRCKLEEMGFTDVGPENKPVSLQETYEAKRHEFHGERQRKEEEMKQMFVQRVKEKE
          DLREQTHTRHYELYRRCKLEEMGFTDVGPENKPVSLQETYEAKRH.FHGERQRKEEEMKQMFVQ.VKEKE
Retrocopy DLREQTHTRHYELYRRCKLEEMGFTDVGPENKPVSLQETYEAKRHDFHGERQRKEEEMKQMFVQPVKEKE

Parental  AILKEAERELQAKFEHLKRLHQEERMKLEEK
          AILKEAERELQA.FEHLKRLHQEERMKLEEK
Retrocopy AILKEAERELQANFEHLKRLHQEERMKLEEK

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	3.21 RPM
SRP007412_cerebellum	0.00 RPM	2.55 RPM
SRP007412_heart	0.00 RPM	16.47 RPM
SRP007412_kidney	0.03 RPM	17.63 RPM
SRP007412_liver	0.03 RPM	16.89 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3335 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3335 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3335 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4060
Pan troglodytes	retro_ptro_2753
Gorilla gorilla	retro_ggor_2728

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017754	3 retrocopies	retro_cjac_1736, retro_cjac_2879, retro_cjac_828,
Homo sapiens	ENSG00000186522	1 retrocopy	retro_hsap_4060,
Gorilla gorilla	ENSGGOG00000013659	1 retrocopy	retro_ggor_2728,
Myotis lucifugus	ENSMLUG00000017273	1 retrocopy	retro_mluc_2285,
Nomascus leucogenys	ENSNLEG00000001328	1 retrocopy	retro_nleu_2111,
Pongo abelii	ENSPPYG00000012144	1 retrocopy	retro_pabe_3335 ,
Pongo abelii	ENSPPYG00000017639	1 retrocopy	retro_pabe_3438,