RetrogeneDB ID: retro_pvam_522

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3594:288626..289972(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCP1
• Ensembl ID: ENSPVAG00000005316
• Aliases: None
• Description: t-complex 1 [Source:HGNC Symbol;Acc:11655]

Sequence

>retro_pvam_522
GTCAAACAGAAAATTCATCCCACATTGGTTATTAGTGGCTATCGACTTGCTTGCAAGGAAGCAGTGCGTTATATCAGTGA
AAATCTAATCGTTAAAACAGCTGATCTTAGAAGAGATTGCTTGATTAATGCTGCTAAGACATCGATGTCACCCACAGTGA
TCGGAACAAAAGGTGATTTCTTTGCTAATATGATAGTAGATGCTGTATTCCCTATTAAATACACAGATGTAAGAGGCCAG
CCTCGCTCTCCAGTCTCTTCCATTAATATTCTGAAGGCTCATGGGAGAAGTCAGATGGAGAATCTGCTCATCGATGGCTA
TGCACTCAACTGCCTGGTGGGATCCCAAGGCACGCCCAAGAGAACAGTTAATGCAAAAATTGCTTGCCTTGACTTCAGCC
TGCAGAAGACAGAAGTGAAACTTGGTGTACAGGTAGTTATTACAGATCCTGAAGCAGTGAACCAGATTAGACAGAGAGAA
TCAGACATCACTGAGTTGCAAATCTAGAAGATCCTGGCAACTGCACCAATGTTATTCCAGCCACTGGTAGAATCAATGAC
ATGTGTCTGAAGAATTTTGTGGAGACTGGAGTTATGGCAGTTAGAAGAGTTTTTTAAAAGGGACCTTAAGCGCATTGCTA
AAGCTTCTGGAGCAACTATTGTACCAACCTTGACCAATTTAGAAGGCGGAGAAACTTTTGAAGCTTCAATGTTGGGACAA
GCAGAAGAGGTGGTGCCGGAGAGAATCTGGGATGATGAACTGATCTTGATCAAAAACACTAAGGCTCGTACATTTGCCTC
AATTATCTTACGTGGGGCAAAGGAATTCACGTGTGATGAGATGGAGCGCTCATTACATGATGCTCTTTGTGTGGTGAAGA
GAGTTTTGGAGTCAGATCTGTGGTTCCAGGTGGGGGTGCTGTTTCGGAAGCAGCCCTTTCCATGTACCTCGAAAACTACG
CAACCTGCATGGGGCCTCGGGTACAGATTGCTATTGCAGAGTTTTCAAGATCTCTCTTTATCATTCCTAATACACTGGCA
GTTAATGCTGCCCAGGACTCCACCGATCTGGCTGCTAAGTTAAGAGCTTTTCATAATGAGACTCAAGTTAACCCAGAATG
CAAAAATCTAAAATGGATTGGTCTTGATCTGGTCAATGATAAACCTCGAGCCAACAAACCCACGGGGGTGTTTGAACCAA
CCAGAGTTAAAGTTAAGAGTCTGAAATTTGCAACAGAAGCTGCAACTACCATTCTTCAAACTGATAATCTTATTAAACTA
CATCCCGAAAGCAAAGATAAGCACACAGGTTATGAAGATGGTGTTCACTCAAGAGCCCTTGATGAC

Alignment

ORF - retro_pvam_522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.22 %
• Parental protein coverage: 80.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VKQKIHPTSVISGYRLACKEAVRYISENLIINTDDLGRDCLINAAKTSMSSKVIGINGDFFANMVVDAVL
          VKQKIHPT.VISGYRLACKEAVRYISENLI..T.DL.RDCLINAAKTSMS..VIG..GDFFANM.VDAV.
Retrocopy VKQKIHPTLVISGYRLACKEAVRYISENLIVKTADLRRDCLINAAKTSMSPTVIGTKGDFFANMIVDAVF

Parental  AIKYTDVRGQPRYPVSSINILKAHGRSQMESLLINGYALNCVVGSQGMPKRIVNAKIACLDFSLQKTKMK
          .IKYTDVRGQPR.PVSSINILKAHGRSQME.LLI.GYALNC.VGSQG.PKR.VNAKIACLDFSLQKT..K
Retrocopy PIKYTDVRGQPRSPVSSINILKAHGRSQMENLLIDGYALNCLVGSQGTPKRTVNAKIACLDFSLQKTEVK

Parental  LGVQVVITDPEKLDQIRQRESDITKERIQKILATG-ANVILTTGGIDDMCLKYFVETGAMAVRRV-LKRD
          LGVQVVITDPE...QIRQRESDIT...I.KILAT...NVI..TG.I.DMCLK.FVETG.MAVRRV..KRD
Retrocopy LGVQVVITDPEAVNQIRQRESDITELQI*KILATA<TNVIPATGRINDMCLKNFVETGVMAVRRV>FKRD

Parental  LKRIAKASGATILSTLANLEGEETFEASMLGQAEEVVQERICDDELILIKNTKARTSASVILRGANDFMC
          LKRIAKASGATI..TL.NLEG.ETFEASMLGQAEEVV.ERI.DDELILIKNTKART.AS.ILRGA..F.C
Retrocopy LKRIAKASGATIVPTLTNLEGGETFEASMLGQAEEVVPERIWDDELILIKNTKARTFASIILRGAKEFTC

Parental  DEMERSLHDALCVVKRVLES-KSVVPGGGAV-EAALSIYLENYATSMGSREQLAIAEFARSLLVIPNTLA
          DEMERSLHDALCVVKRVLES..SVVPGGGAV.EAALS.YLENYAT.MG.R.Q.AIAEF.RSL..IPNTLA
Retrocopy DEMERSLHDALCVVKRVLES<RSVVPGGGAVSEAALSMYLENYATCMGPRVQIAIAEFSRSLFIIPNTLA

Parental  VNAAQDSTDLVAKLRAFHNEAQVNPERKNLKWIGLDLVNGKPRDNKQAGVFEPTLVKVKSLKFATEAAIT
          VNAAQDSTDL.AKLRAFHNE.QVNPE.KNLKWIGLDLVN.KPR.NK..GVFEPT.VKVKSLKFATEAA.T
Retrocopy VNAAQDSTDLAAKLRAFHNETQVNPECKNLKWIGLDLVNDKPRANKPTGVFEPTRVKVKSLKFATEAATT

Parental  ILRIDDLIKLHPESKDDKHGGYEDAVHSGALDD
          IL..D.LIKLHPESK.DKH.GYED.VHS.ALDD
Retrocopy ILQTDNLIKLHPESK-DKHTGYEDGVHSRALDD

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_522 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 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015405	1 retrocopy	retro_amel_828,
Callithrix jacchus	ENSCJAG00000011792	2 retrocopies	retro_cjac_1867, retro_cjac_2193,
Equus caballus	ENSECAG00000017953	1 retrocopy	retro_ecab_798,
Homo sapiens	ENSG00000120438	1 retrocopy	retro_hsap_3722,
Gorilla gorilla	ENSGGOG00000014063	1 retrocopy	retro_ggor_2514,
Microcebus murinus	ENSMICG00000007998	1 retrocopy	retro_mmur_795,
Macaca mulatta	ENSMMUG00000012846	1 retrocopy	retro_mmul_1696,
Oryctolagus cuniculus	ENSOCUG00000013847	1 retrocopy	retro_ocun_1577,
Pongo abelii	ENSPPYG00000017146	1 retrocopy	retro_pabe_3135,
Pan troglodytes	ENSPTRG00000018760	1 retrocopy	retro_ptro_2617,
Pteropus vampyrus	ENSPVAG00000005316	1 retrocopy	retro_pvam_522 ,
Rattus norvegicus	ENSRNOG00000014160	1 retrocopy	retro_rnor_2091,
Sorex araneus	ENSSARG00000002463	1 retrocopy	retro_sara_624,
Sarcophilus harrisii	ENSSHAG00000015128	1 retrocopy	retro_shar_830,
Ictidomys tridecemlineatus	ENSSTOG00000005572	1 retrocopy	retro_itri_1274,