RetrogeneDB ID: retro_pvam_568

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3798:44372..45023(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTP1
• Ensembl ID: ENSPVAG00000008586
• Aliases: None
• Description: glutathione S-transferase pi 1 [Source:HGNC Symbol;Acc:4638]

Sequence

>retro_pvam_568
GCCATCTTCGTCTGCACTACAACCATGCTGCCCTACACCATTGTCTACTTCCCTGTTTGAGGGCGCTGTGAGGCCATGCA
CATGCTGCTGGCTGATCAGGGCTAGAGCTGGAAGGAGGAGGTTGTTACCAAGGAGAACTGGCTGCAGGGCTCACTCAAGG
CCTCCTGTCTATATAAACAGCTCCCCAAGTTCCAGGATAGAGACCTCACCCTGTACCAGTCCAATGCCATCCTGTACTAC
TTGGGCCGCCCCCTCAATCTGTATGAGAAGGACCAGTTGGAGGCAGCCCTGGTGGACGTGGTGAATGATGGCATGAAGGA
CATCCACTGCAAATACATCACCCTCATCTACACCAACTATGAGACGGGCAAGGAGGACTATGTGAAGGAGCTACCAGGGT
GCCTGAAGTCTTTTGAGATCCTGCTGTCCCAGGACCAGGGGGGCCAGGCCTTCATCGTGGGCAACCAGATGTTTGTGGAC
TGCAACCTGCTGGACTTGCTGTTGAATCACTAGATTCTGGCCCGCAGCTGCCTGGATTCCTTCCCCCTACTCTCAGCCTA
TGTGGCTTGCCTCAGTGCCCAGCCTAAGCTCAAGGACTTTCTGGCCTCCCCCAAGCATGTGAACCTACCTATCAGTGGCA
ACAGGAAACAG

Alignment

ORF - retro_pvam_568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.44 %
• Parental protein coverage: 97.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AFFVCAATMPPYAIVYFPVQGRCEAMRMLLADQGQSWKEEVVTKETWLQGPLKASCLYGQLPKFQDGDLT
          A.FVC..TM.PY.IVYFPV.GRCEAM.MLLADQG.SWKEEVVTKE.WLQG.LKASCLY.QLPKFQD.DLT
Retrocopy AIFVCTTTMLPYTIVYFPV*GRCEAMHMLLADQG*SWKEEVVTKENWLQGSLKASCLYKQLPKFQDRDLT

Parental  LYQSNAILRHLGRSLGLYGKDQREAALVDMVNDGVEDLRCKYGTFIYTNYEAGKENYVKELPEHLKPFET
          LYQSNAIL..LGR.L.LY.KDQ.EAALVD.VNDG..D..CKY.T.IYTNYE.GKE.YVKELP..LK.FE.
Retrocopy LYQSNAILYYLGRPLNLYEKDQLEAALVDVVNDGMKDIHCKYITLIYTNYETGKEDYVKELPGCLKSFEI

Parental  LLAQNQGGQAFIVGNQISFADYNLLNLLLNHQVLAPSCLDSFPLLSAYVARLSARPKLKAFLASPEHVNL
          LL.Q.QGGQAFIVGNQ..F.D.NLL.LLLNH..LA.SCLDSFPLLSAYVA.LSA.PKLK.FLASP.HVNL
Retrocopy LLSQDQGGQAFIVGNQM-FVDCNLLDLLLNH*ILARSCLDSFPLLSAYVACLSAQPKLKDFLASPKHVNL

Parental  PINGNNKQ
          PI.GN.KQ
Retrocopy PISGNRKQ

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_568 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 8 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001020	3 retrocopies	retro_amel_1921, retro_amel_249, retro_amel_778,
Canis familiaris	ENSCAFG00000011349	4 retrocopies	retro_cfam_143, retro_cfam_2043, retro_cfam_46, retro_cfam_617,
Macropus eugenii	ENSMEUG00000001519	2 retrocopies	retro_meug_1519, retro_meug_1762,
Mustela putorius furo	ENSMPUG00000004029	2 retrocopies	retro_mputfur_1215, retro_mputfur_1463,
Mus musculus	ENSMUSG00000038155	1 retrocopy	retro_mmus_521,
Pteropus vampyrus	ENSPVAG00000008586	6 retrocopies	retro_pvam_1119, retro_pvam_1463, retro_pvam_568 , retro_pvam_664, retro_pvam_681, retro_pvam_718,
Pteropus vampyrus	ENSPVAG00000009559	1 retrocopy	retro_pvam_1047,
Rattus norvegicus	ENSRNOG00000018237	4 retrocopies	retro_rnor_2140, retro_rnor_2567, retro_rnor_2842, retro_rnor_769,