RetrogeneDB ID: retro_pabe_2791

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:160370395..160371061(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LXN
• Ensembl ID: ENSPPYG00000014245
• Aliases: None
• Description: latexin [Source:HGNC Symbol;Acc:13347]

Sequence

>retro_pabe_2791
ATAGAAATCTCATGGACCCATGACCCAGCCTCCAAGGCAGCCTCGGTGGCAGTGAACTACCTCAACTACCAGCAGGGGAC
ACTCCACAAGGTATTTCTGAGGCAGACAGTCAAACAAGCCAGCACGGAGGATATTCCGGGAAAAGGACATAGGTATCACC
TCAAATGTTCTGTGGAATAAGTTATTCCAAAACAAGTTACAGTGAACTGCATAGCTGAATTGCCTTACCCTGCAGTGGGA
CAAGATACTGCACCAGAAATCAACATCACATGTGAAGGAGAAATGGAAAGAGCCCAGATGAAGAAAACAACACATCTGAT
CAAAAACTCAAGTCCATGAAGGAATCACTAGAAGCATAAAATATTCCAGACATTTTGAGAAATGTATCTCCAAAACATGA
AGCCAGGTCAACATTTAGCCTGGGTTGCCCATGGTTATATAACATGGCAAAATTCTACTGAAAACACGTGATATAAAAGT
GGTAAAAATTAAACTGTCAAGGAAATGCAAAAAAATGATGACTTTATCGAATAGACTATACCATTCCACTTAATGGCATT
GCATCCCAGGAGATTGGTTCCTTGGCAAATGCAAGTTCTTTGGCACTGACAAGATGGTGCTAAAGTAAAATGTAATCGCT
GTCTGCCAAGGGAAGTACAAGTGGAA

Alignment

ORF - retro_pabe_2791 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEIPPTNYPASRAALVAQNYINYQQGTPHRVFEVQKVKQASMEDIPGRGHKYRLKFAVEEIIQKQVKVNC
          .EI..T..PAS.AA.VA.NY.NYQQGT.H.VF..Q.VKQAS.EDIPG.GH.Y.LK..VE..I.KQV.VNC
Retrocopy IEISWTHDPASKAASVAVNYLNYQQGTLHKVFLRQTVKQASTEDIPGKGHRYHLKCSVE*VIPKQVTVNC

Parental  TAEVLYPSTGQETAPEVNFTFEGE-TGKNPDEEDNTFYQRLKSMKEPLEAQNIPDNFGNVSPE-MTLILH
          .AE..YP..GQ.TAPE.N.T.EGE..GK.PDEE.NT..Q.LKSMKE.LEA.NIPD...NVSP..M....H
Retrocopy IAELPYPAVGQDTAPEINITCEGE<NGKSPDEENNTSDQKLKSMKESLEA*NIPDILRNVSPK>MKPGQH

Parental  LAWVACGYIIWQNSTEDTWYKMVKIQTVKQVRRNDDFIE-LDYTILLHNIASQEI-IPWQMQVLWHPQYG
          LAWVA.GYI.WQNSTE.T.YK..K..TVK....NDDFIE..DYTI.L..IASQEI..PWQMQVLWH.Q.G
Retrocopy LAWVAHGYITWQNSTENT*YKSGKN*TVKEMQKNDDFIE<IDYTIPLNGIASQEI>VPWQMQVLWH*QDG

Parental  TKVKHNSCLPKEVQLE
          .KVK.N.CLP.EVQ.E
Retrocopy AKVKCNRCLPREVQVE

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	0.55 RPM
SRP007412_cerebellum	0.00 RPM	4.99 RPM
SRP007412_heart	0.00 RPM	0.93 RPM
SRP007412_kidney	0.00 RPM	5.90 RPM
SRP007412_liver	0.00 RPM	1.84 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2791 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2791 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2791 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3397
Pan troglodytes	retro_ptro_2308
Gorilla gorilla	retro_ggor_2300
Macaca mulatta	retro_mmul_2114

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009336	2 retrocopies	retro_btau_569, retro_btau_860,
Canis familiaris	ENSCAFG00000009096	1 retrocopy	retro_cfam_1863,
Callithrix jacchus	ENSCJAG00000000386	1 retrocopy	retro_cjac_1890,
Homo sapiens	ENSG00000079257	1 retrocopy	retro_hsap_3397,
Gorilla gorilla	ENSGGOG00000003092	1 retrocopy	retro_ggor_2300,
Macaca mulatta	ENSMMUG00000004963	1 retrocopy	retro_mmul_2114,
Nomascus leucogenys	ENSNLEG00000004229	1 retrocopy	retro_nleu_1949,
Pongo abelii	ENSPPYG00000014245	1 retrocopy	retro_pabe_2791 ,
Pan troglodytes	ENSPTRG00000015571	1 retrocopy	retro_ptro_2308,
Pteropus vampyrus	ENSPVAG00000013608	2 retrocopies	retro_pvam_94, retro_pvam_962,
Tupaia belangeri	ENSTBEG00000017673	3 retrocopies	retro_tbel_2746, retro_tbel_3329, retro_tbel_4516,