RetrogeneDB ID: retro_pabe_1294

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:50752619..50753938(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IFT80
• Ensembl ID: ENSPPYG00000014255
• Aliases: None
• Description: intraflagellar transport 80 homolog (Chlamydomonas) [Source:HGNC Symbol;Acc:29262]

Sequence

>retro_pabe_1294
AAAGTATCTTTGAACTCTGCACACTTAGTTGTTTCAATGTCTCTTCAATGTTATGTGGTCTCCACAAAGAACTGGAATAC
ACCAATTATATTTGATCTCAAAGAAGGAACTGTTAGTTTTATCCTGCAGGCAGAAAGACATTTTCTTCTTGTAGATGTTA
GTAGTATCGATTTATATTCATATGAAGGGCCCTTTATTTCATCTCCAAAATTTCCTGGAGTGAGAACAGATATTCTGAAT
GCACAGACTGTGTCTCTGAGTAATGATACCATAGCAATGAGACAAAGCTGATGAAAAAATAATCTTTTTCTTCAAGGTAT
CAACTGGAAAACTATTAGATGATGGAAAGCTTCTTCCTCGTAAGGATGAAATCTTGAAAATTGCTCTGGATCAGAAAGGA
CTTACCAATGATAGAAAAGTCGTTTTCATTGATAAAAATAGAAATATCTATATCACATCTGTGAAACAATTTGAGAAGGA
AGAAAAAATTCTCAAACTTGGTACAATGGTGCATACTTTGGCATGGAGTGGTACATGCAATGTCCTTTGCAGACTTCAGG
ATACTCAACTTACAGTGTGGTATTATTCCAATACGGTTTATGTGGACAGTGACACTTTGCCTAAAACATTACATGAAAGG
GATACAAATGAATTCAGTAAAAATTCCCAAATTGTGAGTTTTGTTGGAAATCAGGTAACTATAACAAGAGTTAATAGCCC
TCTGGTTCACATCAGTGTATCACCATATCCTGTTATTCTCCCTGAATATGTAGGCAGTTCAAAATGGGAAGATGATGTAA
GACTTTGCTGCTTTGTTGAGGAGCAAACCATGTGAGCTTGTCTAGCTGCTATGGCAGTTGCTAATCAAAATATTACTATT
ACAGAAACAGGCTATGCAGCAATTGGTGAAATTGATAAGTTTCAGCACATCAATTCTATAAAAAGTCTTTCATTTAAAGA
GTCAAAAAATGGCCCACATACTAAGGTTTAGTGGGAACATACAGGAGGCTGAAATAGCACTTATTTAGGCTGGCCTCATT
ATCAAGCAATCCAGATCAATATTAATCTCTACAACTGAGAAAGGGCACTGGAATTGGCTGCAAAATACAAAACACGTGTT
GATACAGTTGTTGCTTACTGTCAAAAGAAAAGTTTTTGGAGACATTTGGTAAAGAGGAAACATAAACAATACTTGCAGTA
TGCAGAAGGTCTCCAAATAGATTGAGAGAAAAATCAAAGCCAAAATTGAGATTGAAATTACAAAAGAAGGAGAACAATCA
TCAAGCAGCCAATCCAGTAAGAGTATGGGTCTAAAGCCC

Alignment

ORF - retro_pabe_1294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.11 %
• Parental protein coverage: 56.5 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KASLNYAHLVVSTSLQCYVFSTKNWNTPIIFDLKEGTVSLILQAERHFLLVDGSSIYLYSYEGRFISSPK
          K.SLN.AHLVVS.SLQCYV.STKNWNTPIIFDLKEGTVS.ILQAERHFLLVD.SSI.LYSYEG.FISSPK
Retrocopy KVSLNSAHLVVSMSLQCYVVSTKNWNTPIIFDLKEGTVSFILQAERHFLLVDVSSIDLYSYEGPFISSPK

Parental  FPGMRTDILNAQTVSLSNDTIAIRDK-ADEKIIFLFEASTGKPLGDGKFLSHKNEILEIALDQKGLTNDR
          FPG.RTDILNAQTVSLSNDTIA.R.......I.F.F..STGK.L.DGK.L..K.EIL.IALDQKGLTNDR
Retrocopy FPGVRTDILNAQTVSLSNDTIAMRQS>DEKIIFF-FKVSTGKLLDDGKLLPRKDEILKIALDQKGLTNDR

Parental  KIAFIDKNRDLCITSVKRFGKEEQIIKLGTMVHTLAWNDTCNILCGLQDTRFIVWYYPNTVYVDRDILPK
          K..FIDKNR...ITSVK.F.KEE.I.KLGTMVHTLAW..TCN.LC.LQDT...VWYY.NTVYVD.D.LPK
Retrocopy KVVFIDKNRNIYITSVKQFEKEEKILKLGTMVHTLAWSGTCNVLCRLQDTQLTVWYYSNTVYVDSDTLPK

Parental  TLYERDASEFSKNPHIVSFVGNQVTIRRADGSLVHISISPYPAILHEYVSSSKWEDAVRLCRFVKEQTMW
          TL.ERD..EFSKN..IVSFVGNQVTI.R....LVHIS.SPYP.IL.EYV.SSKWED.VRLC.FV.EQTM.
Retrocopy TLHERDTNEFSKNSQIVSFVGNQVTITRVNSPLVHISVSPYPVILPEYVGSSKWEDDVRLCCFVEEQTM*

Parental  ACLAAMAVANRDMTTAEIAYAAIGEIDKVQYINSIKNLPSKES-KMAHILLFSGNIQEAEIVLLQAGLV-
          ACLAAMAVAN...T..E..YAAIGEIDK.Q.INSIK.L..KES.KMAHIL.FSGNIQEAEI.L..AGL..
Retrocopy ACLAAMAVANQNITITETGYAAIGEIDKFQHINSIKSLSFKES>KMAHILRFSGNIQEAEIALI*AGLI<

Parental  YQAIQININLYNWERALELAVKYKTHVDTVLAYRQKFLETFGKQETNKRYLHY---AEGLQIDWE-KIKA
          YQAIQININLYN.ERALELA.KYKT.VDTV.AY.QK....F...........Y...AEGLQID.E.KIKA
Retrocopy YQAIQININLYN*ERALELAAKYKTRVDTVVAYCQK--KSFWRHLVKRKHKQYLQYAEGLQID*E>KIKA

Parental  KIEMEITKEREQSSSSQSSKSMGLKP
          KIE.EITKE.EQSSSSQSSKSMGLKP
Retrocopy KIEIEITKEGEQSSSSQSSKSMGLKP

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	9.73 RPM
SRP007412_cerebellum	0.24 RPM	10.82 RPM
SRP007412_heart	0.00 RPM	3.73 RPM
SRP007412_kidney	0.00 RPM	6.93 RPM
SRP007412_liver	0.00 RPM	1.77 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1294 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1294 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1294 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,