RetrogeneDB ID: retro_pvam_3

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_613:57533..59558(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000006721
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KIF2C
• Ensembl ID: ENSPVAG00000009856
• Aliases: None
• Description: kinesin family member 2C [Source:HGNC Symbol;Acc:6393]

Sequence

>retro_pvam_3
ATGGCCAGCCAGTTATGCCTCCCTGTCGCCCCGAGCCTCTCGTCCTTGAAAACCGTGAAGCCCCACTTCCGAGACATCCA
AGTGGGCATCTGCGTGGCGATCCAGCGCAGCGACGGGCGGATCCACCTTGCTCTGATCACAGAGTTCAAAAGAGAAAACT
CTTGCGTCACGGTGGAGTGGGTCGAAAAAGGAGTGAAAAAGGGCAAAAAAATTGATCTAGAGACTATATTCCTTCTGAAT
CCAGCACTAGCCTCTGCTGAACACCCCAAACCATCCAGATCATTGGCTTCCTTGTCTGTAGCGCCCTCTTCGACCATCCG
AAATCGATGCATGGCTACGAGTTGGATTGCTACGATCCCACAGAAAAACGAAACACCTTCAGAGGAGAGCCTGACTGTGA
AAGTCCCCAGCAGACCTTGCCTGATGAAGCAGAAAAAGTCTCCCTGCCTCCGAGAAATTGAGAAACTGCAAAAGCAGCGG
GAGAAGCGCAGACGGCTGCAGCTGGAGATCCGAGCCCAACGCGCCCTCAACGTCCACACGGGAAACCCCAACTACGAGAT
CATGCGCATGATTGACGAGTACCGCAGGCAGCTGGACAGCAGCAAGATGTCCAGCCTGGAGCCGCGGGAAGACCGTCGGA
TCTATGTCTGTGTGAGGAAGCGGCCTCTCAACCAGCAGGAGACCACCATGAAGGACCTGGATATCATCACCATCCCTTCG
CACAATGTGGTCATGGTGCATGAGTCTAAGCAGAAGGTGGACCTCACTCGCTACCTGGAAAATCAGACATTCTGCTTCGA
CCATGCCTTCGATGACACGGCCTCCAACGAGTTAGTGTACCAGTTCACCGCCCAGCCGCTGGTGGAGTCTATCTTCCGCA
AGGGCATGGCCACCTGTTTTGCCTATGGGCAGACAGGCAGTGGGAAAACACACACCATGGGTGGAGCCTTTTCAGGAAGG
GACCAAGATTGTTCGAAAGGCATTTACTCACTGGTGGCGCAGGATGTCTTCCTTCTGCTCAAAACTTCGGTTTATAAGAA
GTTGGACCTCAAAGTCTATGGGACATTTTTTGAGATTTATGGGGGCAAGGTATATGATTTGTTGAACTGGAAGAAGAAGC
TGCAGGTCCTTGAGGATGGCAATCAGCAAATCCAGGTAGTCGGGTTGCAGGAGCAGGAGGTGTGTTGTGTGGAGGACGTG
CTGAACCTCGTGGAACTGGGGAACAGCTGCCGGACTTCTGGACAGACATCAGTCAATGCCCACTCCTCCAGGAGCCACGC
CGTGTTCCAGATCATCCTAAAGTCGCGAGGGAAACTGCATGGCAAGTTTTCTCTTGTTGACTTAGCTGGGAATGAAAGGG
GAGCAGATACTGCCAAGGTCAACCGGCAAAGACAGCTGGAGGGGGCGGAGATTAATAAGAGTCTCCTCGCGCTCAAGGAA
TGCATCCGAGCTTTGGGTCAGAATAAGTCTCACACCCCGTTTAGAGCCAGCAAACTCACACAGGTGCTCCGGGACTCCTT
TATCGGCCAGAACTCCTTCACTTGCATGATTGCTACTATTTCTCCAGGGATGGCTTCTTGTGAAAACACCCTCAACACCT
TAAGGTATGCAAATAGAGTAAAAGAATTAACTCTAAATTTAAGGTCCCACCATCGTTGTCTCTATCAGGTTGGACAAGAA
GTGCCAAGGATGTTGGAAAATCACATTGGGAATTCAGAAATGCCCCTTCGGAAAGAGGAATTTATTAAAATACCTTGTAT
ACAGAGTGAGGAAGAGGAAGAGACTAACGAAATTGGAACGTTATCCACCCCATTAATGGAAAATACAACAAGCTCATGGA
AAGAATCAGGCCAGGGGCTGGAGGACAACATCCAGGAGAGAACTGATGGGGTAAACTATGATGTTTATTTTTGCATTACC
CAGCTATTGTCCATTTTGGAGCAGAAAATAGGTATTCTGACTGAAATTCAAAAGAAACTGAAATTATTGCGAGCCAACCT
CCAAAAGAAGAGAAAGGTAGAATGA

Alignment

ORF - retro_pvam_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.04 %
• Parental protein coverage: 63.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELPASANSRKQFSV-PAGPARPSCPAVAEIPLTMVSEEVEEQVHSIRGSSSANPVNSVRRKSCIVKEMEK
          E.P....S....SV.P....R..C.A...I.......E......S........P......KS....E.EK
Retrocopy EHPKPSRSLASLSVAPSSTIRNRCMATSWIATIPQKNETPSE-ESLTVKVPSRPCLMKQKKSPCLREIEK

Parental  MKNKREEKRAQNSEMRIKRAQEYDNSFPNWEFARMIKEFRATLDCHPLTMTDPIEEHRICVCVRKRPLNK
          ....RE..R....E.R..RA.......PN.E..RMI.E.R..LD........P.E..RI.VCVRKRPLN.
Retrocopy LQKQREKRRRLQLEIRAQRALNVHTGNPNYEIMRMIDEYRRQLDSSKMSSLEPREDRRIYVCVRKRPLNQ

Parental  QELTKKEIDVISVPSKCLLFVHEPKLKVDLTKYLENQAFCFDFAFDETASNEVVYRFTARPLVHTIFQGG
          QE.T.K..D.I..PS.....VHE.K.KVDLT.YLENQ.FCFD.AFD.TASNE.VY.FTA.PLV..IF..G
Retrocopy QETTMKDLDIITIPSHNVVMVHESKQKVDLTRYLENQTFCFDHAFDDTASNELVYQFTAQPLVESIFRKG

Parental  KATCFAYGQTGSGKTHTMGGDLSGKAQNASKGIYAMASRDVFLLKNQPRYRNLGLEVYVTFFEIYNGKLF
          .ATCFAYGQTGSGKTHTMGG..SG..Q..SKGIY.....DVFLL.....Y..L.L.VY.TFFEIY.GK..
Retrocopy MATCFAYGQTGSGKTHTMGGAFSGRDQDCSKGIYSLVAQDVFLLLKTSVYKKLDLKVYGTFFEIYGGKVY

Parental  DLLNKKAKLRVLEDGKQQVQVVGLQEHLVTCADDVIKMIDIGSACRTSGQTFANSNSSRSHACFQILLRA
          DLLN.K.KL.VLEDG.QQ.QVVGLQE..V.C..DV......G..CRTSGQT..N..SSRSHA.FQI.L..
Retrocopy DLLNWKKKLQVLEDGNQQIQVVGLQEQEVCCVEDVLNLVELGNSCRTSGQTSVNAHSSRSHAVFQIILKS

Parental  KGRVHGKFSLVDLAGNERGADTSSADRQTRMEGAEINKSLLALKECIRALGQNKAHTPFRESKLTQVLRD
          .G..HGKFSLVDLAGNERGADT....RQ...EGAEINKSLLALKECIRALGQNK.HTPFR.SKLTQVLRD
Retrocopy RGKLHGKFSLVDLAGNERGADTAKVNRQRQLEGAEINKSLLALKECIRALGQNKSHTPFRASKLTQVLRD

Parental  SFIGENSRTCMIAMISPGISSCEYTLNTLRYADRVKELS
          SFIG.NS.TCMIA.ISPG..SCE.TLNTLRYA.RVKEL.
Retrocopy SFIGQNSFTCMIATISPGMASCENTLNTLRYANRVKELT

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_3 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000028678	1 retrocopy	retro_mmus_1251,
Otolemur garnettii	ENSOGAG00000006916	1 retrocopy	retro_ogar_1892,
Pongo abelii	ENSPPYG00000001427	1 retrocopy	retro_pabe_88,
Pteropus vampyrus	ENSPVAG00000009856	1 retrocopy	retro_pvam_3 ,
Pteropus vampyrus	ENSPVAG00000017206	1 retrocopy	retro_pvam_313,
Sus scrofa	ENSSSCG00000003931	1 retrocopy	retro_sscr_25,
Tursiops truncatus	ENSTTRG00000000748	1 retrocopy	retro_ttru_1318,
Drosophila melanogaster	FBgn0030268	2 retrocopies	retro_dmel_1, retro_dmel_2,