RetrogeneDB ID: retro_pvam_108

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1399:56244..57243(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPI
• Ensembl ID: ENSPVAG00000012955
• Aliases: None
• Description: mannose phosphate isomerase [Source:HGNC Symbol;Acc:7216]

Sequence

>retro_pvam_108
ATGGCTGCTCAGCGAGTATTCTCACTTTCCTGCGTGGTGCAGCAGTATGACTAGGGGAAGATGGGTTCCAACGGTGAAGT
GGCTCGGCTGCTGGCCAGCAGTGACCCACTGGCCTGGATCTCAGGCGATAAGCCATATGCAGAGCTGTGGATGAGGACAT
ACCCTCAGGGAGACGCCCAAATTCGTGACAACCATATCTCACAGAAGACCCTAGGCCAGTGGATTGCTGACAACCAGTAC
TACTTGGGCTCGAAGGTCAAGGAAACCTTTAATGGCAAGCAGCCCTTCCTCTTCAAAGTGTTCTTGGTTGAAATGGCCCT
GTCCATCCAGGCACACCCTAACAAGAAGCTGGCAGAGAAGCTGAACCTCCAGGCTTCACAGCACTACCCTGATGCCAACA
AGTCAGAGATGGCCATTGCCCTCACCTCCTTCTAGGGCTTATGTGGCTTCTGGCCAGTTGAAGGGATTGTGACCTTTCTG
ACGAAAGTGCCCAAGTTCCATTTCCTAATTGGAGATAATGCAGCAACACAGGTGAGGCAGAGCCCGAACTGTGACTCCCA
GGTGTGACCTCTGCTCTGCAGGGCTGTTTCTCCCAACTGATGAAGAGTGAGAAGGTGGTGGTAGAACAGCTCAATCTCTC
GGTAAAACAGATCTCCTAGCACGTGGATGCTGGAAACAGGGAGGACATCTAAGGGGAGCTCTTGCTGCAGCTGTACCATC
TGTATTCCAGTGATATCAGAGGCTTTGCCATCTACTTCCTGAACCCGCTTACCTTGGAGCTGGAAGAGGCCATGTTTCTG
GAGGCCAATGTGCCTCAAGCCTACCTGAAAGAGACTGCATGGAGTGCACAGTATGTTCAGACAACACGGTATGTGCTGGC
CTGACACCCAAGTTCATCCATGTGCAACTCTGTATGACATGCTCAGCTAGAACCCCAGCCTCAGCAAGGATAGTCTCTTT
TCTCCAACATGGAGTCAGGAAGACCCCTATCTCTCTTTG

Alignment

ORF - retro_pvam_108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 79.67 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASQRVFPLSCVVQQYAWGKMGSNSEVARLLASSDPRAGISEDKPYAELWMGTHPRGDAKILDNRISQKT
          MA.QRVF.LSCVVQQY..GKMGSN.EVARLLASSDP.A.IS.DKPYAELWM.T.P.GDA.I.DN.ISQKT
Retrocopy MAAQRVFSLSCVVQQYD*GKMGSNGEVARLLASSDPLAWISGDKPYAELWMRTYPQGDAQIRDNHISQKT

Parental  LGQWIAENQDCLGSKVKDTFNGKLPFLFKVLSVETALSIQAHPNKELAEKLHLQAPQHYPDANHKPEMAI
          LGQWIA.NQ..LGSKVK.TFNGK.PFLFKV..VE.ALSIQAHPNK.LAEKL.LQA.QHYPDAN.K.EMAI
Retrocopy LGQWIADNQYYLGSKVKETFNGKQPFLFKVFLVEMALSIQAHPNKKLAEKLNLQASQHYPDAN-KSEMAI

Parental  ALTSFQGLCGFRPAEEIVTFLMKVPEFHFLIGDNAATQLKQSLSRDSQT-VASALKNCFSHLMKSEKKVV
          ALTSF.GLCGF.P.E.IVTFL.KVP.FHFLIGDNAATQ..QS...DSQ..V.SAL..CFS.LMKSE.KVV
Retrocopy ALTSF*GLCGFWPVEGIVTFLTKVPKFHFLIGDNAATQVRQSPNCDSQV<VTSALQGCFSQLMKSE-KVV

Parental  VEQLNLLVKRISQQVAAGNNVEDICGELLLQLHQQYPGDIGCFAIYFLNLLTLKPGEAMFLEANVPHAYL
          VEQLNL.VK.IS..V.AGN..EDI.GELLLQL...Y..DI..FAIYFLN.LTL...EAMFLEANVP.AYL
Retrocopy VEQLNLSVKQIS*HVDAGNR-EDI*GELLLQLYHLYSSDIRGFAIYFLNPLTLELEEAMFLEANVPQAYL

Parental  K-GDCVECMACSDNTVRAGLTSKFIDV-PTLCEMLSYTPSPSKERLFPPTQSQEDPYLSI
          K..DC.EC..CSDNTV.AGLT.KFI.V..TL..MLS..PS.SK..LF.PT.SQEDPYLS.
Retrocopy K<RDCMECTVCSDNTVCAGLTPKFIHV<ATLYDMLS*NPSLSKDSLFSPTWSQEDPYLSL

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_108 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000012955	1 retrocopy	retro_pvam_108 ,