RetrogeneDB ID: retro_pvam_132

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1553:3517..4210(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VTI1B
• Ensembl ID: ENSPVAG00000011671
• Aliases: None
• Description: vesicle transport through interaction with t-SNAREs 1B [Source:HGNC Symbol;Acc:17793]

Sequence

>retro_pvam_132
ATGGCTACCTCGGCCACCTCCTCTGAACATTTTGAGAAACTACATGAGATCTTCCGCGGCCTCCATGAAGACCTACGACG
GGTGCCGGAACGGCTCCTGGGGACTGCAGGAACAAAAGAGAAGAAGTTGATCAGAGATTTTGATGAAAAGTAACAGAAAG
CAAATGAAACGCTGGCAGAGACGGAAGAGGAACTACACTATGCACTCTTATCTTTCCGTAACCCTATGATGTCTAAGCTT
CGAACCTACTGGAGTGACCTTGCCAAATTCCACCGGGAAGTGAGAAGCATACCTTTGACAGCCCCACCTAGGGGTTGAGG
AGACATGAAATATGGCACATATGCTGTAGAGAATGAGCATATGAATCGGCTACAGTCTCAAAAGGCGTTACTTCTGCAAG
GCACTGACAGCCTGAACGGGGCTACCCAGAGTACTGAGCTTTCTAATCAGATTGCCACAGAGACTGACCAGATTGGCTCA
GAAATCATAGAAGAGCTGGGGAAGCAACGTGAAAAGTTGGAATGAATCAAGAATAGACTGGTAAACACAGGTAAAAACTT
GAGCAAAAGTCCGAAGGTTCTCTGGTCAATGTCCAGAGAAGTGACAACCAACAAGCTACTACTTTCCATCATCATCTTAC
TTGAGCTACCCATCCTGGTAGGCCTGGTTTATTACAAATTCTTTTGTTAGCAT

Alignment

ORF - retro_pvam_132 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATSAASSEHFEKLHEIFRGLHEDLRRVPERLLGAAGTEEKKKLIRDFDEKQQEANETLSEMEEELRYAP
          MATSA.SSEHFEKLHEIFRGLHEDLRRVPERLLG.AGT.EKK.LIRDFDEK.Q.ANETL.E.EEEL.YA.
Retrocopy MATSATSSEHFEKLHEIFRGLHEDLRRVPERLLGTAGTKEKK-LIRDFDEK*QKANETLAETEEELHYAL

Parental  LSFRNPMTSKIRTYRRDLAKLHREVRSTPLTATPGGRGDMKYGTYAVENEHMNRLQSQRALLLQGTDSLN
          LSFRNPM.SK.RTY..DLAK.HREVRS.PLTA.P.G.GDMKYGTYAVENEHMNRLQSQ.ALLLQGTDSLN
Retrocopy LSFRNPMMSKLRTYWSDLAKFHREVRSIPLTAPPRG*GDMKYGTYAVENEHMNRLQSQKALLLQGTDSLN

Parental  RTTQSIERSHRIATETDQIGSEIIEELGEQRDQLERTKNRLVNTGENLSKSRKILRSMSRKVTTNKLLLS
          ..TQS.E.S..IATETDQIGSEIIEELG.QR..LE..KNRLVNTG.NLSKS.K.L.SMSR.VTTNKLLLS
Retrocopy GATQSTELSNQIATETDQIGSEIIEELGKQREKLE*IKNRLVNTGKNLSKSPKVLWSMSREVTTNKLLLS

Parental  IIILLELAILGGLVYYKFFRKH
          IIILLEL.IL.GLVYYKFF..H
Retrocopy IIILLELPILVGLVYYKFFC*H

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_132 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 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015263	1 retrocopy	retro_cjac_1439,
Dasypus novemcinctus	ENSDNOG00000003643	2 retrocopies	retro_dnov_1503, retro_dnov_2031,
Dipodomys ordii	ENSDORG00000015939	2 retrocopies	retro_dord_52, retro_dord_716,
Echinops telfairi	ENSETEG00000006101	1 retrocopy	retro_etel_783,
Felis catus	ENSFCAG00000014090	1 retrocopy	retro_fcat_1855,
Homo sapiens	ENSG00000100568	3 retrocopies	retro_hsap_1002, retro_hsap_2682, retro_hsap_3013,
Gorilla gorilla	ENSGGOG00000005620	2 retrocopies	retro_ggor_1871, retro_ggor_797,
Macropus eugenii	ENSMEUG00000004910	2 retrocopies	retro_meug_499, retro_meug_697,
Microcebus murinus	ENSMICG00000010843	1 retrocopy	retro_mmur_849,
Myotis lucifugus	ENSMLUG00000011184	3 retrocopies	retro_mluc_1299, retro_mluc_2393, retro_mluc_781,
Macaca mulatta	ENSMMUG00000015866	1 retrocopy	retro_mmul_1420,
Mustela putorius furo	ENSMPUG00000007130	1 retrocopy	retro_mputfur_1516,
Nomascus leucogenys	ENSNLEG00000000780	4 retrocopies	retro_nleu_1184, retro_nleu_2241, retro_nleu_231, retro_nleu_83,
Pongo abelii	ENSPPYG00000005927	5 retrocopies	retro_pabe_2298, retro_pabe_2498, retro_pabe_2602, retro_pabe_845, retro_pabe_974,
Pan troglodytes	ENSPTRG00000006468	3 retrocopies	retro_ptro_1808, retro_ptro_2037, retro_ptro_751,
Pteropus vampyrus	ENSPVAG00000011671	3 retrocopies	retro_pvam_132 , retro_pvam_592, retro_pvam_797,
Tupaia belangeri	ENSTBEG00000003049	1 retrocopy	retro_tbel_3432,
Tarsius syrichta	ENSTSYG00000007688	2 retrocopies	retro_tsyr_1662, retro_tsyr_94,