RetrogeneDB ID: retro_pvam_541

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3659:3680..4405(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSPVAG00000007494
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 2 [Source:HGNC Symbol;Acc:3293]

Sequence

>retro_pvam_541
AACAAGTTCGACGCATTGAAAGATGAAGACAGCGGGGCCATGATCAGAAGGAAGAAAAAGGCACACAGAAAGATGGTGAG
AAGGAAAAAATGGAACGAGACAAGAGTCAGAGCAGCAGCCAGAGGAAGGCTGTTGTCCCTGGACCAGCAAAGCATCCCCT
ACAGTACAACTACACTTTCTGGCACTCCAGGAGAACCCCCCGCTGGTCCCACCAGCTCACAGAGCTACAAGCAGACTATT
AAACTGATGGGCGCTTTTGCCACTGTGGTATGTCCTGGGCACCTGATAGCCAAATGGTATGTCCTGGGGACCTGATAGGC
CACAACAACTTCTATCTCTTCAAAGGAGGAATTAAAACCATGTGGGAGGATGATGCAAATAAAAATGGTGGCAAGTGGAA
TACTTGGCTAAAAAAGGGCTTGGACTCCTGTTGCTACGAGAATCTCATCCTGGCCATGTTGGAGCAGTTCATGGTTGTGG
GGGATATCTTTGGGGCTGTGGTCTCCAACCACTTTCAGGAAAACATTCTTTCCATATGGAATAAGACTGCCAGCGACCAA
GCCACCACAGCACGAATCCAGGATACGCTTCGGCGAGTGCTTAACCTACCTCCCAACACCATTTTGGAATACAAAACCCA
CAGTGACAGCATCAAAATGCCAGGCAGCCTGGGCTCCCAAAAACTCCTTTTCCAAAATCTCTAGAAGCTGCGGTTGAATG
TGCCA

Alignment

ORF - retro_pvam_541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.02 %
• Parental protein coverage: 99.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NKFDALKDDDSG-DHDQNEENSTQKDGEKEKMERDKSQSISKRKAVVPGPAEHPLQYNYTFWYSRRT-PG
          NKFDALKD.DSG..HDQ.EE..TQKDGEKEKMERDKSQS.S.RKAVVPGPA.HPLQYNYTFW.SRRT.P.
Retrocopy NKFDALKDEDSG<GHDQKEEKGTQKDGEKEKMERDKSQSSSQRKAVVPGPAKHPLQYNYTFWHSRRT>PA

Parental  RPTSSQSYEQNIKQIGTFASV-EQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRL
          .PTSSQSY.Q.IK..G.FA.V....W...S.MV.PGDL.GH..F.LFK.GIK.MWEDDANKNGGKW...L
Retrocopy GPTSSQSYKQTIKLMGAFATV<GMSWAPDSQMVCPGDLIGHNNFYLFKGGIKTMWEDDANKNGGKWNTWL

Parental  RKGLASRCWENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVLNLPPN
          .KGL.S.C.ENLILAML.EQFMV...I.GAVVS..FQE.I.SIWNKTASDQATTARI.DTLRRVLNLPPN
Retrocopy KKGLDSCCYENLILAML-EQFMVVGDIFGAVVSNHFQENILSIWNKTASDQATTARIQDTLRRVLNLPPN

Parental  TIMEYKTHTDSIKTPGRLGPQRLLFQNLWKPRLNVP
          TI.EYKTH.DSIK.PG.LG.Q.LLFQNL.K.RLNVP
Retrocopy TILEYKTHSDSIKMPGSLGSQKLLFQNL*KLRLNVP

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_541 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 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Callithrix jacchus	ENSCJAG00000013786	2 retrocopies	retro_cjac_1061, retro_cjac_2717,
Macropus eugenii	ENSMEUG00000015519	2 retrocopies	retro_meug_445, retro_meug_644,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Monodelphis domestica	ENSMODG00000002680	1 retrocopy	retro_mdom_1717,
Otolemur garnettii	ENSOGAG00000009155	1 retrocopy	retro_ogar_104,
Pteropus vampyrus	ENSPVAG00000007494	4 retrocopies	retro_pvam_1147, retro_pvam_340, retro_pvam_541 , retro_pvam_720,
Tursiops truncatus	ENSTTRG00000010927	2 retrocopies	retro_ttru_1799, retro_ttru_1920,