RetrogeneDB ID: retro_pvam_1091

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_2802:15919..17375(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMEK1
• Ensembl ID: ENSPVAG00000015294
• Aliases: None
• Description: SMEK homolog 1, suppressor of mek1 (Dictyostelium) [Source:HGNC Symbol;Acc:20219]

Sequence

>retro_pvam_1091
TCCCGTCTCCGCGTCAAACTTCATGGCCTGAACGAAGACCAACAATGGACTGATCTAGGCACTGGGTACGTCTCCTCTGC
CTACGTGGAACGACTCCAGGGCGTGTCTCTGCTAGTTCAGTCAGAGTCCAACGGCTCACTGATCTTGGAGTCAAAGATAA
ATCCAAACACTCCGTATAAGAAGAAACGGGGCCTATTGATAGTTTGGTCTGAAGGTGAGAACCATGGAATGGCATTGAGT
TTCCAGGACACAGCCGGGTGTCACGAGATCTGGGAAGACATTTGCCGGGTTCAAGGAATAGACCCATCCGTCGACATCAC
ACAAGACTTCTTGGATATTTCAGAAGATGAATTTGATGAAATTCCAGAAACTAGTAATATGGTTGACCTCCCGAACTGTG
AACTCGGTAAGCTTAAACAGATTGCTACCATAGTTACCTCAGCTCTCACTTCGCCTATCCGTAAGGAAAGGCTGGCCCTG
ATCTTGGAAAATGAGGACTATATTAAAAAGCTACTGCAGCTGTTCCACACTTGTGAGAGCCTAGGAGACACTGAAGGCTT
ACAGCATTTGCATGTAATTATGAAAGGAATCTTATTCCTCAACAAGACGTGTCTGTTCGAGATAATGTTTTCTGATGAGT
GTATCATGAATGTGGTGGGGTGCCTTGAATATGACCCTGCTTTGGCTGAGCCAAAAAGGCACAGGGAATTCTTGACCCAA
AATGCAAAGTTCAAGGAAGTGATACCAATAACAGACTGTGAACTTAGGCAAAAAATACATCAGACGTACAGGGTGCAGTA
CATTCACAACATCCTTTTCCCTGTACCATCCGTATTGGAAGAGAATTGTCTTTCTACTATCGCAAATTTTATTTTTCCTC
AACAAGGTTGAGATAATCCGCATGATACAGAAAGATGACAGTTTTGCCTGAAGTTTTTCACAGTTGAAGGATGAGACTAC
AGATGATGATAAACGGCGTGACTTGGTATTTTTTTTCAAGGAATTCTGTTCATTTTCTCAGTCACTGCAGCCTCAAAGCA
AAGGTGCACTATTCAGAACATTGACAAAATTGGGAATTCTTCCTGCTCTTAAAATTGTAATGATCCTGGATGACTTGCAA
ATAAGGTCAGCTGCTGCTGACATACTTGCTCATCTAGTGGAGTATAATCCATCCATGATCCGAGGATCAATGCTACAAGA
ATACAAGCGGAATGAAGACTGTAAACTTTTCATTCATTTACTAATTGAACAAATGATCTGTGATACCGACCCTGAGCTAG
GAGGTGCTCTTCATTTAATGGGACTTCTTCGTTCTCTACTTGATCCAGAAAACATGCTGGTGACACCTAATAAATGTGAA
AGAACTGAATTTCTACATTTCTTCTATAAACAGTGTATGCATAAACTCGTAGCACCACTTTTGGCCACTACAGAAGATAC
ATGTGAAAAGGATAAT

Alignment

ORF - retro_pvam_1091 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.21 %
• Parental protein coverage: 59.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TRRRVKVYTLNEDRQWDDRGTGHVSSGYVERLKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLIVWS
          .R.RVK...LNED.QW.D.GTG.VSS.YVERL.G.SLLV..ES.GSL.LESKINPNT.Y.K....LIVWS
Retrocopy SRLRVKLHGLNEDQQWTDLGTGYVSSAYVERLQGVSLLVQSESNGSLILESKINPNTPYKKKRGLLIVWS

Parental  EAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVDITQDLVDESEEERFDDM--SSPGLELPSCELSRLE
          E.EN...ALSFQ..AGC.EIWE.IC.VQG.DPSVDITQD..D.SE.E.FD.....S....LP.CEL..L.
Retrocopy EGENHGMALSFQDTAGCHEIWEDICRVQGIDPSVDITQDFLDISEDE-FDEIPETSNMVDLPNCELGKLK

Parental  EIAELVASSLPSPLRREKLALALENEGYIKKLLELFHVCEDLENIEGLHHLYEIIKGIFLLNRTALFEVM
          .IA..V.S.L.SP.R.E.LAL.LENE.YIKKLL.LFH.CE.L...EGL.HL..I.KGI..LN.T.LFE.M
Retrocopy QIATIVTSALTSPIRKERLALILENEDYIKKLLQLFHTCESLGDTEGLQHLHVIMKGILFLNKTCLFEIM

Parental  FSEECIMDVIGCLEYDPALSQPRKHREFLTKTAKFKEVIPISDPELKQKIHQTYRVQYIQDMVLPTPSVF
          FS.ECIM.V.GCLEYDPAL..P..HREFLT..AKFKEVIPI.D.EL.QKIHQTYRVQYI.....P.PSV.
Retrocopy FSDECIMNVVGCLEYDPALAEPKRHREFLTQNAKFKEVIPITDCELRQKIHQTYRVQYIHNILFPVPSVL

Parental  EENMLSTLHSFI-FFNKVEIVGMLQEDEKFLTDLFAQLTDEATDEEKRQELVNFLKEFCAFSQTLQPQNR
          EEN.LST...FI.F.NKVEI..M.Q.D..F....F.QL.DE.TD..KR..LV...KEFC.FSQ.LQPQ..
Retrocopy EENCLSTIANFI>FLNKVEIIRMIQKDDSFA*S-FSQLKDETTDDDKRRDLVXXXKEFCSFSQSLQPQSK

Parental  DAFFKTLSNMGILPALEVILGMDDTQVRSAATDIFSYLVEYNPSMVREFVMQEAQQNDDDILLINLIIEH
          .A.F.TL...GILPAL......DD.Q.RSAA.DI...LVEYNPSM.R....QE...N.D..L.I.L.IE.
Retrocopy GALFRTLTKLGILPALKIVMILDDLQIRSAAADILAHLVEYNPSMIRGSMLQEYKRNEDCKLFIHLLIEQ

Parental  MICDTDPELGGAVQLMGLLRTLVDPENMLATANKTEKTEFLGFFYKHCMHVLTAPLLANTTEDKPSKDD
          MICDTDPELGGA..LMGLLR.L.DPENML.T.NK.E.TEFL.FFYK.CMH.L.APLLA.TTED...KD.
Retrocopy MICDTDPELGGALHLMGLLRSLLDPENMLVTPNKCERTEFLHFFYKQCMHKLVAPLLA-TTEDTCEKDN

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_1091 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000012467	1 retrocopy	retro_dord_714,
Erinaceus europaeus	ENSEEUG00000006324	1 retrocopy	retro_eeur_316,
Pan troglodytes	ENSPTRG00000006638	1 retrocopy	retro_ptro_124,
Pteropus vampyrus	ENSPVAG00000015294	1 retrocopy	retro_pvam_1091 ,
Tupaia belangeri	ENSTBEG00000008535	1 retrocopy	retro_tbel_2368,
Tarsius syrichta	ENSTSYG00000010333	1 retrocopy	retro_tsyr_863,
Tursiops truncatus	ENSTTRG00000013598	1 retrocopy	retro_ttru_1398,
Vicugna pacos	ENSVPAG00000002765	1 retrocopy	retro_vpac_536,