RetrogeneDB ID: retro_ptro_2308

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:158976002..158976668(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LXN
• Ensembl ID: ENSPTRG00000015571
• Aliases: None
• Description: latexin [Source:HGNC Symbol;Acc:13347]

Sequence

>retro_ptro_2308
ATAGAAATTTCATGGACCCATGACCCAGCCTCCAAGGCAGCCTCGGTGGCAGTGATCTGCCTCAACTACCAGCAAGGGAC
ACCCCACAAGGTATTTCTGAGGGAGACAGTCAAACAAACCAGCACGGAGGATATCCCAGGAAAAGGACATAAGTATCACC
TCAAATGTTCTGTGGAATAAGTTATTCTAAAACAAGTTGCAGTGAACTGCATAGCTGAATTGCCTTACCCTGCAGTGGGA
CAAGATACTGTACCAGAAATCAACATCACATGTGAAGGAGAAATTTAAAGAGCCCAGATAAAGAAAACAACACGTCTGAT
CAAAAACTCAAGTCCATGAAGGAATCACTAGAAGCACAAAATATTCCAGACATTTTGAGAAATGTATCTCCAAAACATGA
AGCCAGGTCAACATTTAGCCTGGGTTGCCTGTGGTTATGTAACATGGCAAAATTCTGCTGAAAACACGTGATATAAAAGT
GGTAAAAATTAAACTGTCAAGGAAATGCAAAAAAATGATGACTTTATTGAATAGACTATACCATTCCACTTCATGACATT
GCATCCCAGGAGATTGATTCCTTGGGAAATGCAAGTTCTTTGGCACTGACAAGATGGTGCTAAAGTAAAATGTAATCGCT
GTCTGCCAAGGGAAGTACAAGCGGAA

Alignment

ORF - retro_ptro_2308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEIPPTNYPASRAALVAQNYINYQQGTPHRVFEVQKVKQASMEDIPGRGHKYRLKFAVEEIIQKQVKVNC
          .EI..T..PAS.AA.VA....NYQQGTPH.VF....VKQ.S.EDIPG.GHKY.LK..VE..I.KQV.VNC
Retrocopy IEISWTHDPASKAASVAVICLNYQQGTPHKVFLRETVKQTSTEDIPGKGHKYHLKCSVE*VILKQVAVNC

Parental  TAEVLYPSTGQETAPEVNFTFEGE-TGKNPDEEDNTFYQRLKSMKEPLEAQNIPDNFGNVSPE-MTLVLH
          .AE..YP..GQ.T.PE.N.T.EGE...K.PD.E.NT..Q.LKSMKE.LEAQNIPD...NVSP..M....H
Retrocopy IAELPYPAVGQDTVPEINITCEGE<NLKSPDKENNTSDQKLKSMKESLEAQNIPDILRNVSPK>MKPGQH

Parental  LAWVACGYIIWQNSTEDTWYKMVKIQTVKQVQRNDDFIE-LDYTILLHNIASQEI-IPWQMQVLWHPQYG
          LAWVACGY..WQNS.E.T.YK..K..TVK..Q.NDDFIE..DYTI.LH.IASQEI.IPW.MQVLWH.Q.G
Retrocopy LAWVACGYVTWQNSAENT*YKSGKN*TVKEMQKNDDFIE<IDYTIPLHDIASQEI>IPWEMQVLWH*QDG

Parental  TKVKHNSRLPKEVQLE
          .KVK.N..LP.EVQ.E
Retrocopy AKVKCNRCLPREVQAE

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	2.25 RPM
SRP007412_cerebellum	0.00 RPM	3.87 RPM
SRP007412_heart	0.00 RPM	4.37 RPM
SRP007412_kidney	0.00 RPM	9.44 RPM
SRP007412_liver	0.00 RPM	3.90 RPM
SRP007412_testis	0.00 RPM	1.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2308 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2308 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2308 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3397
Gorilla gorilla	retro_ggor_2300
Pongo abelii	retro_pabe_2791
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,