RetrogeneDB ID: retro_ptro_2951

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: AACZ03172276.1:509..1827(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IFT80
• Ensembl ID: ENSPTRG00000015578
• Aliases: None
• Description: intraflagellar transport 80 homolog (Chlamydomonas) [Source:HGNC Symbol;Acc:29262]

Sequence

>retro_ptro_2951
AAAGTATCTTTGAACTCTGCACACTTAGTTGTTTCAATGTCTCTTCAATGTTATGTGGTCTCCACAAAGAACTGGAATAC
ACCAATTACATTTGATCTCAAAGAAGGAACAGTTAGTTTTATCCTGCAGGCAGAAAGACATTTTCTTCTTGTAGATGTTA
GTAGTATCGATTTATATTTATATGAAGGGCCCTTTATTTCATCTCCAAAATTTCCTGCAGTGAGAACAGATATTCTGAAT
GCACAGACTGTGTCTATGAGTAATGATACCATAGCAATGAGACAAAGCTGATGAAAAAATAATCTTTTTCTTCAAGGTAT
CAACTGGAAAACTATTAGATGATGGAAAGCTTCTTCCTCGTAAGGATGCAATCTTGAAAATTGCTCTGGATCAAAAAGGA
CTTACCAATGACAGAAAAGTCACTTTCATTGATAAAAATAGAGATATCTATATCACTTCTGTGAAACAATTTGGGAAGGA
AGAAAAAATTCTCAAACTTGGAACAATGGTGCATACTTTGGCATGGAGTGATACATGCAATGTCCTTTGCAGGCTTCAGG
ATACTCAATTTACAGTGTGGTATTATTCCAATATGGTTTATGTGGACAGTGACACTTTGCCTAAAACATTACATGAAAGG
GATACAAATAAATTCAGTAAAAATTCCCAAATTGTGAGTTTTCTTGGAAATCAGGTAACTATAACAAGAGTTAACGGCCC
TCTGGTTCACATCAGTGTATCACCATATCCTGTTATTCTCCCTGAATATGCAGGCAGTTCAAAATGGGAAGATGATGTAA
GACTTTGCTGCTTTGTTAAGGAGCAAACCATGTGAGCTTGTCTACCTGCTATGGCAGTTGCTAATCAAAATATTACTATT
ACAGAAATAGGCTATGCAGCAATTGGTGAAATTGATAAGTTTCAGTACATCAATTCTATAAAAAGTCTTTCATTTAAAGA
GTCAAAAAATGGTCCACATACTAAAGTTTAGTGGAAACATACAGGAGGCTGAAATAGCACTTCTTCAGGCTGGCCTCATT
GTCAAGCAATCCAGATCAATATTAATCTCTACAACTGAAAAGGGCACTGGAATTGGCTGCAAAATACAAAACACATGTTG
ATACGGTTGTTGCTTAGTGTCAAAAGAAAAGTTTTTGGAGACATTTGGTAAAGAGGAAACATAAACAATACTTGCAGCAT
GCAGAAGGTCTCCAAATAGATTGAGAGAAAAATCAAAGCCAAAATTGGGATTGAAATTACAAAAGAAGGAGAACAATCAT
CAAGCAGCCAATCCAGTAAGAGTATGAGTCTAAAGCCC

Alignment

ORF - retro_ptro_2951 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.38 %
• Parental protein coverage: 56.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KASLNYAHLVVSTSLQCYVFSTKNWNTPIIFDLKEGTVSLILQAERHFLLVDGSSIYLYSYEGRFISSPK
          K.SLN.AHLVVS.SLQCYV.STKNWNTPI.FDLKEGTVS.ILQAERHFLLVD.SSI.LY.YEG.FISSPK
Retrocopy KVSLNSAHLVVSMSLQCYVVSTKNWNTPITFDLKEGTVSFILQAERHFLLVDVSSIDLYLYEGPFISSPK

Parental  FPGMRTDILNAQTVSLSNDTIAIRDK-ADEKIIFLFEASTGKPLGDGKFLSHKNEILEIALDQKGLTNDR
          FP..RTDILNAQTVS.SNDTIA.R.......I.F.F..STGK.L.DGK.L..K..IL.IALDQKGLTNDR
Retrocopy FPAVRTDILNAQTVSMSNDTIAMRQS>DEKIIFF-FKVSTGKLLDDGKLLPRKDAILKIALDQKGLTNDR

Parental  KIAFIDKNRDLCITSVKRFGKEEQIIKLGTMVHTLAWNDTCNILCGLQDTRFIVWYYPNTVYVDRDILPK
          K..FIDKNRD..ITSVK.FGKEE.I.KLGTMVHTLAW.DTCN.LC.LQDT.F.VWYY.N.VYVD.D.LPK
Retrocopy KVTFIDKNRDIYITSVKQFGKEEKILKLGTMVHTLAWSDTCNVLCRLQDTQFTVWYYSNMVYVDSDTLPK

Parental  TLYERDASEFSKNPHIVSFVGNQVTIRRADGSLVHISISPYPAILHEYVSSSKWEDAVRLCRFVKEQTMW
          TL.ERD...FSKN..IVSF.GNQVTI.R..G.LVHIS.SPYP.IL.EY..SSKWED.VRLC.FVKEQTM.
Retrocopy TLHERDTNKFSKNSQIVSFLGNQVTITRVNGPLVHISVSPYPVILPEYAGSSKWEDDVRLCCFVKEQTM*

Parental  ACLAAMAVANRDMTTAEIAYAAIGEIDKVQYINSIKNLPSKES-KMAHILLFSGNIQEAEIVLLQAGLVY
          ACL.AMAVAN...T..EI.YAAIGEIDK.QYINSIK.L..KES.KM.HIL.FSGNIQEAEI.LLQAGL..
Retrocopy ACLPAMAVANQNITITEIGYAAIGEIDKFQYINSIKSLSFKES>KMVHILKFSGNIQEAEIALLQAGLIV

Parental  -QAIQININLYN-WERALELAVKYKTHVDTVLAYRQKFLETFGKQETNKRYLHY---AEGLQIDWE-KIK
          .QAIQININLYN...RALELA.KYKTHVDTV.A..QK....F...........Y...AEGLQID.E.KIK
Retrocopy <QAIQININLYN<LKRALELAAKYKTHVDTVVA*CQK--KSFWRHLVKRKHKQYLQHAEGLQID*E>KIK

Parental  AKIEMEITKEREQ-SSSQSSKSIGLKP
          AKI..EITKE.EQ.SSSQSSKS..LKP
Retrocopy AKIGIEITKEGEQSSSSQSSKSMSLKP

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	7.58 RPM
SRP007412_cerebellum	0.00 RPM	6.02 RPM
SRP007412_heart	0.00 RPM	3.35 RPM
SRP007412_kidney	0.03 RPM	7.74 RPM
SRP007412_liver	0.00 RPM	4.19 RPM
SRP007412_testis	0.00 RPM	60.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2951 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2951 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2951 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000068885	1 retrocopy	retro_hsap_1568,
Macaca mulatta	ENSMMUG00000017282	1 retrocopy	retro_mmul_2216,
Pongo abelii	ENSPPYG00000014255	1 retrocopy	retro_pabe_1294,
Pan troglodytes	ENSPTRG00000015578	2 retrocopies	retro_ptro_1055, retro_ptro_2951 ,