RetrogeneDB ID: retro_ggor_2300

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:142132458..142133124(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LXN
• Ensembl ID: ENSGGOG00000003092
• Aliases: None
• Description: None

Sequence

>retro_ggor_2300
ATAGAAATTTCATGGACCCATGACCCAGCCTCCAAGGCAGCCTCGGTGGCAGTGATCTGCCTCAACTACCAGCAAGGGAC
ACCCCACAAGGTATTTCCGAGGGAGACAGTCAAACAAACCAGCACGGAGGATATCCCAGGAAAAGGACATAAGTATCACC
TCAAATGTTCTGTGGAATAAGTTATTCTAAAACAAGTTGCAGTGAACTGCATAGCTGAATTGCCTTACCCTGCAGTGGGA
CAAGATACTGTACCAGAAATCAACATCACATGTGAAGGAGAAATGGAAAGAGCCCAGATGAAGAAAACAACACATCTGAT
CAAAAACTCAAGTCCATGAAGGAATCACTAGAAGCACAAAATATTCCAGACATTTTAAGAAATGTATCTCCAAAACATGA
AGCCAGGTCAACATTTAGCCTGGGTTGCCTGTGGTTATGTAACATGGCAAAATTCTGCTGAAAACACGTGATATAAAAGT
GGTAAAAATTAAACTGTCAAGGAAATGCAAAAAAATGATGACTTTATCGAATAGACTATACCATTCCACTTCATGACATT
GCATCCCAGGAGACTGATTCCTTGGCAAATGCAAGTTCTTTGGCACTGACAAGATGGTGCTAAGGTAAAATGTAATCGCT
GTCTGCCAAGGGAAGTACAAGCGGAA

Alignment

ORF - retro_ggor_2300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.6 %
• 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 IEISWTHDPASKAASVAVICLNYQQGTPHKVFPRETVKQTSTEDIPGKGHKYHLKCSVE*VILKQVAVNC

Parental  TAEVLYPSTGQETAPEVNFTFEGE-TGKNPDEDDNTFYQRLKSMKEPLEAQNIPDNFGNVSPE-MTLVLH
          .AE..YP..GQ.T.PE.N.T.EGE..GK.PDE..NT..Q.LKSMKE.LEAQNIPD...NVSP..M....H
Retrocopy IAELPYPAVGQDTVPEINITCEGE<NGKSPDEENNTSDQKLKSMKESLEAQNIPDILRNVSPK>MKPGQH

Parental  LAWVACGYIIWQNSTEDTWYKMVKIQTVKQVQRNDDFIE-LDYTILLHNIASQE-IIPWQMQVLWHPQYG
          LAWVACGY..WQNS.E.T.YK..K..TVK..Q.NDDFIE..DYTI.LH.IASQE..IPWQMQVLWH.Q.G
Retrocopy LAWVACGYVTWQNSAENT*YKSGKN*TVKEMQKNDDFIE<IDYTIPLHDIASQE>LIPWQMQVLWH*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	0.48 RPM
SRP007412_cerebellum	0.00 RPM	0.71 RPM
SRP007412_heart	0.00 RPM	2.19 RPM
SRP007412_kidney	0.00 RPM	6.50 RPM
SRP007412_liver	0.00 RPM	5.14 RPM
SRP007412_testis	0.00 RPM	4.97 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2300 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3397
Pan troglodytes	retro_ptro_2308
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,