RetrogeneDB ID: retro_pabe_1439

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:19303374..19304121(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KYNU
• Ensembl ID: ENSPPYG00000012827
• Aliases: None
• Description: kynureninase [Source:HGNC Symbol;Acc:6469]

Sequence

>retro_pabe_1439
GATATCCCTGAAGCAATTGAGAAGGGAGGAGGCTCGATTACAGCAATCCTGTTTAGTGGGCTGCATTTTTATATTGGGCA
GCTCTTTAATATACCTGCTACCATTAAAGCTGGACAAGTGAAGAGATGTTTTGCTGGCTTGATCTAGCATGTACAGTTGG
AAATGCTGAACTCCACTTACATGACCGAAGAGTTGACTTTGCCCACTGGTGTTCCCACAATAATTTGAATGCAGGAGCAG
GAGGTCTGGCAGGTGCTTTTTCTATGAAAAGCAGCCCGTATGATTAAAGCTGTGCTGGTGGGTGGTTTGGCTGTGAACTC
AGCACCAGATTTGAGATGGATAACCAACTGCAGTTAATCCCTGGGGTTAGTGGATTCCAAATTTCAAATCCTTCCATTTT
GTTGGTCTATTTCTTACACACTAGTTTAGAGATCTTTAGGCAGGCAGCGATTAAAGCATTGTGGAGAAAATCTATTTTGC
TGACTGGTTATCTGGAATACCTGATCTAGCACTGCTATGGCAAAAATAAAGCAGAATCAAATAAGCCAATGGTGACCATT
ACTGCATCCCATATGGAGGATCAGGGCTGCCAGCTGACACTAACATTTTTCTGTTCCAAAGAAAGATGTTTTCCAAGAGG
TAGAAAACAGAGGAGTGGTTTATGACAAGTGGAATCCAAATGTCATTCAAGTGGCTCCAGTTCCTTTCTATCATTATTTC
CATGATGTTTATACATTTATCAATCTG

Alignment

ORF - retro_pabe_1439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.14 %
• Parental protein coverage: 53.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DILEVIEKEGDSIAVILFSGVHFYTGQHFNIPAITKAGQAKGCYVGF-DLAHAVGNVELYLHDWGVDFAC
          DI.E.IEK.G.SI..ILFSG.HFY.GQ.FNIPA..KAGQ.K.C..G..DLA..VGN.EL.LHD..VDFA.
Retrocopy DIPEAIEKGGGSITAILFSGLHFYIGQLFNIPATIKAGQVKRCFAGL<DLACTVGNAELHLHDRRVDFAH

Parental  WCSYKYLNAGAGGIAGA-FVHEKH-AHTIKPALVG-WFGHELSTRFKMDNKLQLIPGVCGFRISNPPILL
          WCS...LNAGAGG.AGA.F..EK..A..IK..LVG.WFG.ELSTRF.MDN.LQLIPGV.GF.ISNP.ILL
Retrocopy WCSHNNLNAGAGGLAGA<FFYEKQ<ARMIKAVLVG<WFGCELSTRFEMDNQLQLIPGVSGFQISNPSILL

Parental  VCSLHASLEIFKQATMKALRKKSILLTGYLEYLIKHSYGKDKAATKKPVVNIITPSHIEERGCQLTIT-F
          V..LH.SLEIF.QA..KAL..KSILLTGYLEYLI.H.YGK.KA...KP.V..IT.SH.E..GCQLT.T.F
Retrocopy VYFLHTSLEIFRQAAIKALWRKSILLTGYLEYLI*HCYGKNKAESNKPMVT-ITASHMEDQGCQLTLT>F

Parental  SVPNKDVFQELEKRGVVCDKRNPNGIRVAPVPLYNSFHDVYKFTNL
          SVP.KDVFQE.E.RGVV.DK.NPN.I.VAPVP.Y..FHDVY.F.NL
Retrocopy SVPKKDVFQEVENRGVVYDKWNPNVIQVAPVPFYHYFHDVYTFINL

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	0.17 RPM
SRP007412_cerebellum	0.00 RPM	0.24 RPM
SRP007412_heart	0.03 RPM	0.39 RPM
SRP007412_kidney	0.10 RPM	12.56 RPM
SRP007412_liver	0.03 RPM	64.91 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1439 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1439 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1439 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013126	1 retrocopy	retro_amel_501,
Loxodonta africana	ENSLAFG00000002172	1 retrocopy	retro_lafr_329,
Microcebus murinus	ENSMICG00000017770	1 retrocopy	retro_mmur_940,
Mustela putorius furo	ENSMPUG00000003685	1 retrocopy	retro_mputfur_503,
Pongo abelii	ENSPPYG00000012827	1 retrocopy	retro_pabe_1439 ,