RetrogeneDB ID: retro_pvam_648

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_558:15756..16926(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3L
• Ensembl ID: ENSPVAG00000010103
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit L [Source:HGNC Symbol;Acc:18138]

Sequence

>retro_pvam_648
AATGCTGATGATCCTGATCCCCTTCAACTACCCAACCAGTGGCTCTGGGACATCATTGGTGAGTTTACTTATCAGTTTCA
GTCATTTAGTCAGTACCACTGTAAGACTGCCAAGAAGTTGAAGGAAGAGATTGACTTCTTTCATTCTAATCTCAAAATCT
GGAACATTCACAGTGTCTTCAATGTCCTTCACTCTCTGGTAGACAAGTCCAACATCGATGGGCAGTAGGAGGTGTACAGA
AGTGGAAGTGACCCTGAAAATGTGGCTGTAGAGTACGGGCGACATTACCTATACAAGATGCTTGTATACTTCAGCCTCAC
GGGGCTTTTGCATCTGCACTCCCTGTCGGGGGATTTCTACCAGGCCATCAAGGTGCTGGAGAATATCAAACTGAAAAGAA
GAGTACATACTCTGCACGAGTGCCAGTTTACCAAATATTATTTTACATATTTGGTTTTACATATTTGATGATGCATTGCT
ATCAGGATGCCATCGGGTCTTTGCTAACAACATCCTCCTCTATATCCAGAGGACCAAGAGTGTGTTCCAGAGGACCACAT
ATACGTATGAGATGATTAACAAGCAGAATGAGCAGATGTATGCACTGCTTGCCATCGCTCTCATTGTGTAATCCATATGT
ATCCATGAGAGCATTCACCTCCAGCTGTGGGAGAAATACTGGGATAAGATGCTACGTATGCAGAAAGGTGACCTGTGGGT
CTATGAGGAAATTTTCAGCTATTCTTGCCCCAAATTCCTGTTGATGTAGTGCCCAGATATGACAAGATACATCCCAACTA
CCACAAGGAATCCTTTTTGCAGCAGCTGAAGGTGTTTTCTGAAGAAGTGCAGCAGCGAGCCCATCTCTTGACCATTCACA
GTTCCCCCAAGCTTGACACCACCATGCCTGTGGCCAAGCTGGCCAGCTTCCTGGACCTCACAGAGCAGGAGTTCCATATT
CAGCTTCTTATCTTCAAACACCAAATGAAGAACCTGGTGTGGACCAGCTGTACCTCCTCCCTAGATGGCAAATTTCAGTC
AGCCTCTGAGGCTGATTACATCGATAAAAACATGATTCACATCACAGACACCAAGGTTGACAGACGCTATGGCGATTTCT
TCATCTAGCAGATTCACAAATTTGAGGAGCTCAATAAAACTCTGAAGAAG

Alignment

ORF - retro_pvam_648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.53 %
• Parental protein coverage: 64.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NADGPAPLELPNQWLWDIIDEFIYQFQSFSQYRCKTAKKSEEEIDFLRSNPKIWNVHSVLNVLHSLVDKS
          NAD.P.PL.LPNQWLWDII.EF.YQFQSFSQY.CKTAKK..EEIDF..SN.KIWN.HSV.NVLHSLVDKS
Retrocopy NADDPDPLQLPNQWLWDIIGEFTYQFQSFSQYHCKTAKKLKEEIDFFHSNLKIWNIHSVFNVLHSLVDKS

Parental  NINRQLEVYTSGGDPESVAGEYGRHSLYKMLGYFSLVGLLRLHSLLGDYYQAIKVLENIEL-NKKSMYS-
          NI..Q.EVY.SG.DPE.VA.EYGRH.LYKML.YFSL.GLL.LHSL.GD.YQAIKVLENI.L..KKS.YS.
Retrocopy NIDGQ*EVYRSGSDPENVAVEYGRHYLYKMLVYFSLTGLLHLHSLSGDFYQAIKVLENIKL<EKKSTYSA

Parental  RVPECQVTTYYYVGFAYLMMRRYQDAI-RVFA-NILLYIQRTKSMFQRTTYKYEMINKQNEQMHALLAIA
          RVP..Q....Y..GF.YLMM..YQDAI.RVFA.NILLYIQRTKS.FQRTTY.YEMINKQNEQM.ALLAIA
Retrocopy RVPVYQI-LFYIFGFTYLMMHCYQDAI<RVFANNILLYIQRTKSVFQRTTYTYEMINKQNEQMYALLAIA

Parental  LTMYPMRIDESIHLQLREKYGDKMLRMQKGDPQVYEELFSYSCPKFL-SPVVPNYDNVHPNYHKEPFLQQ
          L......I.ESIHLQL.EKY.DKMLRMQKGD..VYEE.FSYSCPKFL...VVP.YD..HPNYHKE.FLQQ
Retrocopy LIV*SICIHESIHLQLWEKYWDKMLRMQKGDLWVYEEIFSYSCPKFL<VDVVPRYDKIHPNYHKESFLQQ

Parental  LKVFSDEVQQQAQLSTIRSFLKLYTTMPVAKLAGFLDLTEQEFRIQLLVFKHKMKNLVWTSGISALDGEF
          LKVFS.EVQQ.A.L.TI.S..KL.TTMPVAKLA.FLDLTEQEF.IQLL.FKH.MKNLVWTS..S.LDG.F
Retrocopy LKVFSEEVQQRAHLLTIHSSPKLDTTMPVAKLASFLDLTEQEFHIQLLIFKHQMKNLVWTSCTSSLDGKF

Parental  QSASEVDFYIDKDMIHIADTKVARRYGDFFIRQIHKFEELNRTLKK
          QSASE.D.YIDK.MIHI.DTKV.RRYGDFFI.QIHKFEELN.TLKK
Retrocopy QSASEAD-YIDKNMIHITDTKVDRRYGDFFI*QIHKFEELNKTLKK

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_648 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001443	3 retrocopies	retro_cfam_1496, retro_cfam_1877, retro_cfam_315,
Monodelphis domestica	ENSMODG00000019068	3 retrocopies	retro_mdom_1247, retro_mdom_1585, retro_mdom_432,
Otolemur garnettii	ENSOGAG00000029444	1 retrocopy	retro_ogar_1635,
Pongo abelii	ENSPPYG00000011806	2 retrocopies	retro_pabe_1135, retro_pabe_1136,
Pteropus vampyrus	ENSPVAG00000010103	1 retrocopy	retro_pvam_648 ,