RetrogeneDB ID: retro_ptro_1481

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:16296162..16296793(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TERF2IP
• Ensembl ID: ENSPTRG00000008365
• Aliases: None
• Description: None

Sequence

>retro_ptro_1481
CGGTCCCTGAAGCCCCCGCGGGGCCAGGAGCACGAGCACTTGCCAGGGGACGCCTGGGGCGCCCCTCCTCCCAGAAGCTC
CCGCGGAAGACTGGAGCAGGCCACCGGGCTGCGGATAATGGGAACCACAGAGTGAGAGGACTCCGCATCGGCCTGAAGGA
AGAGCATGTGAAGGTAGAAATCCGGGAGAGTGAAGAAGCGCTGTAAAAGATGCTTGCAGAAGCCACCCGGGGATTGGAGG
AGGTTGTGGTGGATGAGAGCCCTGATTTGGAAATACATTTAACGATGTGTGATGAGGATCCCCCACGCCTGAGGAAGACT
CAGAAACAGAGCCTCATCAGGAAGAAGAAGAAGAAGAAGAAACAGTTTCTCCACTGGAGGTGGGAGCTGCCATGATGATG
ATTCCGCAGTTAATGGAGAAGTTTAACTTGGATCTATCAACAGTTACACAGGCCTTCCTAAAAAATAGTGGCGAGCCGGA
GGCTGTTTCCTCCTTCGTAGCGTGCGGTCAGAGAGCTGACGGATAACCCATTTGGTCCCAACAAGATGACATAGGTTTGT
AAAAAGATGATGGGGATAACAGAGAGGCATTGGTCAAAATATTTGGTGCTCAGAATATAGCTCAGAGGATT

Alignment

ORF - retro_ptro_1481 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.06 %
• Parental protein coverage: 53.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RYLKHLRGQEHKYLLGDAPVSP-SSQKLKRKAEEDPEAADSG-EPQNKRTPDLPE-EEYVKEEIQENEEA
          R.LK..RGQEH..L.GDA...P.SSQKL.RK......AAD.G.EPQ..RTP..PE.EE.VK.EI.E.EEA
Retrocopy RSLKPPRGQEHEHLPGDAWGAP<SSQKLPRKTGAGHRAADNG<EPQSERTPHRPE>EEHVKVEIRESEEA

Parental  VKKMLVEATREFEEVVVDESPPDFEIHITMCDDDP-PTPEEDSETQPDEEEEEEEEKVSQPEVGAAIKII
          ..KML.EATR..EEVVVDES.PD.EIH.TMCD.DP.PTPEEDSET.P..........VS..EVGAA...I
Retrocopy L*KMLAEATRGLEEVVVDES-PDLEIHLTMCDEDP<PTPEEDSETEPHQXXXXXXXTVSPLEVGAAMMMI

Parental  RQLMEKFNLDLSTVTQAFLKNSGELEATSAFLASGQRADGYPIWSRQDDIDLQKDDEDTREALVKKFGAQ
          .QLMEKFNLDLSTVTQAFLKNSGE.EA.S.F.A.GQRADG.PIWS.QDDI.L.KDD.D.REALVK.FGAQ
Retrocopy PQLMEKFNLDLSTVTQAFLKNSGEPEAVSSFVACGQRADG*PIWSQQDDIGL*KDDGDNREALVKIFGAQ

Parental  NVARRI
          N.A.RI
Retrocopy NIAQRI

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	0.05 RPM	131.88 RPM
SRP007412_cerebellum	0.11 RPM	145.80 RPM
SRP007412_heart	0.06 RPM	30.08 RPM
SRP007412_kidney	0.03 RPM	38.39 RPM
SRP007412_liver	0.10 RPM	22.19 RPM
SRP007412_testis	0.21 RPM	107.28 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1481 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1481 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1481 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1588

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000005519	1 retrocopy	retro_ggor_1588,
Pan troglodytes	ENSPTRG00000008365	1 retrocopy	retro_ptro_1481 ,
Tursiops truncatus	ENSTTRG00000001222	1 retrocopy	retro_ttru_999,