RetrogeneDB ID: retro_pvam_147

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1615:333463..333837(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX8
• Ensembl ID: ENSPVAG00000001001
• Aliases: None
• Description: syntaxin 8 [Source:HGNC Symbol;Acc:11443]

Sequence

>retro_pvam_147
TCCAGCCGGATGACTGGAGGGGCTAAGCTAGGCAACCCAACCATCGGCTCTTCGAGGAGTCAGGGGAGACCAGAGATTTG
GATGAAGTCCTACAACGAGAGCAGAAAACTGTCCAAGAAGAAGATGTGGGCCTCCATGCCCTTTACTCTGTCCTAAGTCT
CCAAAATCAAATGGGGCAGGAAATGGGGAATGAGCTGGATGAGCAAAAATGACATCACCGATGACCTTGCGAACCTGGGG
AGGAGCTCAGATAACACACTTCACACTGAAACCAGACATGTGAATAAGGTGGACAGGAAGTCAGATCTTGTTGGAGGACA
ATAGCAATTTTATTGCTGCTCATGGCTGTTGTACATGTTCCGGTCTGCCCCACC

Alignment

ORF - retro_pvam_147 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.77 %
• Parental protein coverage: 53.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSLMTGGPKLGIP-NPWLFEEPEETRGLGFDEIRQQQQKIIQEQDAGLDALSSIISRQKQMGQEIGNELD
          SS.MTGG.KLG.P.N..LFEE..ETR.L..DE..Q..QK..QE.D.GL.AL.S..S.Q.QMGQE.GNELD
Retrocopy SSRMTGGAKLGNP<NHRLFEESGETRDL--DEVLQREQKTVQEEDVGLHALYSVLSLQNQMGQEMGNELD

Parental  EQ-NEIIDDIANLVENTDEKLRTETRRVNMVDRKS-TSCGMIMVILLLLVAIVVVAVWPT
          EQ.N.I.DD.ANL....D..L.TETR.VN.VDRKS..SC.....ILLLL.A.V.V.V.PT
Retrocopy EQ>NDITDDLANLGRSSDNTLHTETRHVNKVDRKS<RSCWRTIAILLLLMAVVHVPVCPT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_147 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002045	1 retrocopy	retro_amel_911,
Canis familiaris	ENSCAFG00000017413	1 retrocopy	retro_cfam_1959,
Cavia porcellus	ENSCPOG00000002114	1 retrocopy	retro_cpor_1034,
Felis catus	ENSFCAG00000008276	1 retrocopy	retro_fcat_634,
Myotis lucifugus	ENSMLUG00000008612	1 retrocopy	retro_mluc_2329,
Mustela putorius furo	ENSMPUG00000007815	2 retrocopies	retro_mputfur_975, retro_mputfur_996,
Pteropus vampyrus	ENSPVAG00000001001	1 retrocopy	retro_pvam_147 ,
Rattus norvegicus	ENSRNOG00000003849	2 retrocopies	retro_rnor_2422, retro_rnor_2500,
Tarsius syrichta	ENSTSYG00000010795	1 retrocopy	retro_tsyr_1906,