RetrogeneDB ID: retro_pabe_2104

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:24453401..24454125(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: G3BP1
• Ensembl ID: ENSPPYG00000015968
• Aliases: G3BP1, G3BP
• Description: Ras GTPase-activating protein-binding protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5RB87]

Sequence

>retro_pabe_2104
ATGGTGATGGAGAAGGCTAGTCCCCTGCTGGTTGGGTGGGAATTTGTGAGACAGCATTACATACTGCTGAACTAGGCCCC
AGACATTCTGCATAGATTTTATGGAAGGAACTCTTCTTATGTCCATGGGGGATTGGATTCAAATAGAAAGCTAGCAGATG
CAGTTTACGGACAGAAAAAAATGCACAGGAAAGTGATGTCACGAAACTTCACCAACTGCCACACCGAGATTCTCCGTGTT
GATGCTTATGCCACGCTAAATGATGGTGTGGTAGTCCAGGTGTTGGAGCTTCTGTCTAACAACAACCAGGCTTTGAGGAG
ATTCATGCAGATGTTTGTACTTGCTCCTGAGGGGTCTGTTGCAAATCAGTTCTATGTTCACAATGATATCTTCAGATTGC
AAGATGAGGTCTTTGGTGGGTTTGTCACTGAGCCTCAGGAGGAGTCTGAAGAAGTAGTAGAGGAACCTGAAGAAAAGATA
GCAAACACCTCAGGTGGTACCTGATGATTCTGGAACTTCCTGTGATCAGGTAGTTGTCAGCAATGACATGGAAGAACATT
TAGAGGAGCCAGTTGCTGAGCTGGAGCCTGATCCTGAACCAGAACCAGAACAAGAATGTGTATCTGAAATCCAAGAGGAA
AAGTCTGAGCTAGCATTAGAAGAAACTGCTCCTGAGGATGCTCAGAAGAGTTCCTCTCCAGTACCTGCAGACATAGACAG
TACG

Alignment

ORF - retro_pabe_2104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.71 %
• Parental protein coverage: 51.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQKEIHRKVMSQNF
          MVMEK.SPLLVG.EFVRQ.Y.LLN.APD.LHRFYG.NSSYVHGGLDSN.K.ADAVYGQK..HRKVMS.NF
Retrocopy MVMEKASPLLVGWEFVRQHYILLN*APDILHRFYGRNSSYVHGGLDSNRKLADAVYGQKKMHRKVMSRNF

Parental  TNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEVFGG
          TNCHT.I..VDA.ATLNDGVVVQV..LLSNNNQALRRFMQ.FVLAPEGSVAN.FYVHNDIFR.QDEVFGG
Retrocopy TNCHTEILRVDAYATLNDGVVVQVLELLSNNNQALRRFMQMFVLAPEGSVANQFYVHNDIFRLQDEVFGG

Parental  FVTEPQEESEEEVEEPEE-RQQTPEVVPDDSGTFYDQAVVSNDMEEHLEEPVAEPEPDPEPEPEQEPVSE
          FVTEPQEESEE.VEEPEE.R.QTP.VVPDDSGT..DQ.VVSNDMEEHLEEPVAE.EPDPEPEPEQE.VSE
Retrocopy FVTEPQEESEEVVEEPEE>R*QTPQVVPDDSGTSCDQVVVSNDMEEHLEEPVAELEPDPEPEPEQECVSE

Parental  IQEEKPEPVLEETVPEDAQKSSSPAPADIAQT
          IQEEK.E..LEET.PEDAQKSSSP.PADI..T
Retrocopy IQEEKSELALEETAPEDAQKSSSPVPADIDST

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	0.39 RPM	31.96 RPM
SRP007412_cerebellum	0.49 RPM	26.87 RPM
SRP007412_heart	0.12 RPM	45.82 RPM
SRP007412_kidney	0.00 RPM	55.22 RPM
SRP007412_liver	0.09 RPM	66.07 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2104 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2104 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006626	2 retrocopies	retro_cpor_1119, retro_cpor_464,
Dasypus novemcinctus	ENSDNOG00000018758	3 retrocopies	retro_dnov_1492, retro_dnov_1632, retro_dnov_526,
Homo sapiens	ENSG00000145907	1 retrocopy	retro_hsap_2322,
Microcebus murinus	ENSMICG00000012235	2 retrocopies	retro_mmur_1247, retro_mmur_1469,
Mustela putorius furo	ENSMPUG00000013661	1 retrocopy	retro_mputfur_625,
Oryctolagus cuniculus	ENSOCUG00000022143	1 retrocopy	retro_ocun_1352,
Otolemur garnettii	ENSOGAG00000001726	2 retrocopies	retro_ogar_3156, retro_ogar_3183,
Pongo abelii	ENSPPYG00000015968	1 retrocopy	retro_pabe_2104 ,
Pan troglodytes	ENSPTRG00000017438	1 retrocopy	retro_ptro_1696,
Pteropus vampyrus	ENSPVAG00000017250	2 retrocopies	retro_pvam_1188, retro_pvam_188,
Rattus norvegicus	ENSRNOG00000013186	1 retrocopy	retro_rnor_1282,
Tarsius syrichta	ENSTSYG00000004570	1 retrocopy	retro_tsyr_1391,