RetrogeneDB ID: retro_ptro_1696

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:139457403..139458798(-)
• Located in intron of: ENSPTRG00000012492

Retrocopy information

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

Parental gene information

• Parental gene symbol: G3BP1
• Ensembl ID: ENSPTRG00000017438
• Aliases: None
• Description: None

Sequence

>retro_ptro_1696
ATGGTGATGGAGAAGGCTAGTCCCCTGCTGGTTGGGTGGGAATTTGTGAGACAGCATTACACACTGCTGAACTAGGCCCC
AGACATGCTGCATAGATTTTATGGAAGGAACTCTTCTTATGTCCGTGGGGGATTGGATTCAAATAGAAAGCTAGCAGATG
CAGTTTACGGACAGAAAGAAATCCACAGGAAAGTGATGTCACGAAACTTCAGCAACTGCCACACCAAGATTCTCCATGTT
GATGCTTATGCCACGCTAAATGATGGTGTGGTAGTCCAGGTGTTGGGGCTTCTGTCTAACAACAACCAGGCTTTGAGGAG
ATTCATGCAGATGTTCATACTTGCTCCTGAGGGGTCTGTTGCAAATCAGTTCTATGTTCACAATGATATCTTCAGATAGC
AAGATGAGGTCTTTGGTGGGTTTGTCACTGAGCCTCAGGAGGAGTCTGAAGAAGTAGTAGAGGAACCTGAAGAAAAGACA
GCAAACACCTCAGGTGGTACCTGATGATTCTGGAACTTTCTGTGATCAGGCAGTTGTCAGTAATGACGTGGAAGAACATT
TAGAGGAGCCAGTTGCTGAACTGGAGCCTGATCCTGAGCCAGAACCAGAACAAGAATGTGTATCTGAAATCCAAGAGGAA
AAGTCTGAGCTAGTATTAGAAGAAACTGCTCCTGAGGATGCTCAGAAGAGTTCTTCTCCAGCACCTGCAGACATATCTCA
GACAGTACGGGAAGACTTGAGGACATTTTCTTGGGCATCTGTGACCAGTAACAACCTTCAACCCAGTGGAGCTGTTCCAG
TTACTGGGATACCTCCTTATGTTGGTAAAGTACTAGCTTCACAGCCCTGTACAGAGTCTAAGCCTGAATCTCAGATTCCA
CCACAGAAACCTCAAAGGGATCAAAGGATGTGAGAACAACGAAGAAATATTCCTCCCCAAAGGGGACCCAGACCGATCTG
TGAGGCTGGTGAGCAAGGTGACATTGAACCCCAAAGAGTGGTGAGACACCCTGACAGTCACCAACTCTTCATTGGCAACC
TGTCTCATTAAGTGGACAAATCAGAGCTTAAAGATTTCTTTCAAAATTATGGGAACGTGGTGGAGTTGCACATTAACAGT
GGTGGGAAATTACCCAGTTTTGGTTTTGTTTTGATGATTCTGAGCCTGTTCAGAAGGTCCTTCGCAACAGGCCCATCATG
TTCAGAGGTGAGGTCTGTCTGAATGTGGAAGAGAAGAAGCCTCGAGCTGCTAGGGAAGGGGACTGACGAGATGATCGCCT
TAGGGGACCTGGAGGCCCTCTATGTGGGGTGGGTGGTGGAATGAGAGGCCCTCCCCATGGAGGCATGGTGCAGAAAGCAG
GATTTGGAGTGGGAAGAAGGCTTGCTCCATGGCAG

Alignment

ORF - retro_ptro_1696 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQKEIHRKVMSQNF
          MVMEK.SPLLVG.EFVRQ.YTLLN.APDMLHRFYG.NSSYV.GGLDSN.K.ADAVYGQKEIHRKVMS.NF
Retrocopy MVMEKASPLLVGWEFVRQHYTLLN*APDMLHRFYGRNSSYVRGGLDSNRKLADAVYGQKEIHRKVMSRNF

Parental  TNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEVFGG
          .NCHTKI.HVDA.ATLNDGVVVQV.GLLSNNNQALRRFMQ.F.LAPEGSVAN.FYVHNDIFR.QDEVFGG
Retrocopy SNCHTKILHVDAYATLNDGVVVQVLGLLSNNNQALRRFMQMFILAPEGSVANQFYVHNDIFR*QDEVFGG

Parental  FVTEPQEESEEEVEEPEE-RQQTPEVVPDDSGTFYDQAVVSNDVEEHLEEPVAEPEPDPEPEPEQEPVSE
          FVTEPQEESEE.VEEPEE.RQQTP.VVPDDSGTF.DQAVVSNDVEEHLEEPVAE.EPDPEPEPEQE.VSE
Retrocopy FVTEPQEESEEVVEEPEE>RQQTPQVVPDDSGTFCDQAVVSNDVEEHLEEPVAELEPDPEPEPEQECVSE

Parental  IQEEKPEPVLEETAPEDAQKSSSPAPADIAQTVQEDLRTFSWASVTSKNLPPSGAVPVTGIPPHVVKVPA
          IQEEK.E.VLEETAPEDAQKSSSPAPADI.QTV.EDLRTFSWASVTS.NL.PSGAVPVTGIPP.V.KV.A
Retrocopy IQEEKSELVLEETAPEDAQKSSSPAPADISQTVREDLRTFSWASVTSNNLQPSGAVPVTGIPPYVGKVLA

Parental  SQPRPESKPESQIPPQRPQRDQRVREQRINIPPQRGPRPIREAGEQGDIEPRRMVRHPDSHQLFIGNLPH
          SQP..ESKPESQIPPQ.PQRDQR..EQR.NIPPQRGPRPI.EAGEQGDIEP.R.VRHPDSHQLFIGNL.H
Retrocopy SQPCTESKPESQIPPQKPQRDQRM*EQRRNIPPQRGPRPICEAGEQGDIEPQRVVRHPDSHQLFIGNLSH

Parental  EVDKSELKDFFQSYGNVVELRINSGGKLPN-FGFVVFDDSEPVQKVLSNRPIMFRGEVRLNVEEKKTRAA
          .VDKSELKDFFQ.YGNVVEL.INSGGKLP..F.F..FDDSEPVQKVL.NRPIMFRGEV.LNVEEKK.RAA
Retrocopy *VDKSELKDFFQNYGNVVELHINSGGKLPS<FWFC-FDDSEPVQKVLRNRPIMFRGEVCLNVEEKKPRAA

Parental  REGDRRDNRLRGPGGPRGGLGGGMRGPPRGGMVQKPGFGVGRGLAPRQ
          REGD.RD.RLRGPGGP..G.GGGMRGPP.GGMVQK.GFGVGR.LAP.Q
Retrocopy REGD*RDDRLRGPGGPLCGVGGGMRGPPHGGMVQKAGFGVGRRLAPWQ

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	0.11 RPM	23.58 RPM
SRP007412_cerebellum	0.18 RPM	31.33 RPM
SRP007412_heart	0.15 RPM	53.51 RPM
SRP007412_kidney	0.16 RPM	59.13 RPM
SRP007412_liver	0.03 RPM	52.31 RPM
SRP007412_testis	0.63 RPM	108.97 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1696 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1696 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1696 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2322
Gorilla gorilla	retro_ggor_1763

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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,