RetrogeneDB ID: retro_pvam_720

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_951:398925..399661(+)
• Located in intron of: ENSPVAG00000014288

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_720
ATGAACAACAAGTTTGACTCATTGAAAGATGACGACAGTGAAGACCATAGTCAGAATGACAAAAACAGCACACAGAAAGA
TAGTGAGAAGGAAAAAAAAATAGAACAAGACAAGAGTCAGAGCAGCAGCAAGAGGAAGGCTGTTGCCCCTGGACCAGCAG
AGCATCCCCTACAGTACAACTATTCCTTCTGGTACTCCAGGATAACCCCCGGCCGTCCCACCAGCTCACAGAGCTACGAG
CAGAATATTAAACAGATTACACCTTTGCCTCTGTGGAACAGTTGTGGAGGCTTTACAGTCACGTGGTATGTCCCGGGGAC
CTGACAGGCCAGAATGACTTCCATCTCTTTAAAAAAGGAATCAAACCCATGTGGGAGGATGATGCAGATAAAAATGATGG
TTAGTGGATTATTTGGCTATGAAAGGGTGTGGCCTCCCATTGCTGGGAGAAACTCATTCTGGCCATTTTGGGGTATCAGT
TCATGGTTGGGGAGGAGGTCTATGTGGCTGTGGTCTGATCTAGTTTCAGGAGGACATTCTTTCCACATGGAATAAGACTG
CCAGCAACCAAGTCACCACAGGCCAAATCTGGGATATGCTTTGGCGAGTACTTAACCTACCTCCCAACACCATTATGGGA
TAAAAAACCCACACCAATAGCATCAAAATGCCAGGAAGGATGGGCCCCCAAAGGCTCCTTTTTCAAAACCTCTGGAAGCC
GTGGTTGAATGTGCCA

Alignment

ORF - retro_pvam_720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.42 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNNKFDALKDDDSGDHDQNEENSTQKDGEKEKM-ERDKSQSISKRKAVVPGPAEHPLQYNYTFWYSRRTP
          MNNKFD.LKDDDS.DH.QN..NSTQKD.EK....E.DKSQS.SKRKAV.PGPAEHPLQYNY.FWYSR.TP
Retrocopy MNNKFDSLKDDDSEDHSQNDKNSTQKDSEKXXXXEQDKSQSSSKRKAVAPGPAEHPLQYNYSFWYSRITP

Parental  GRPTSSQSYEQNIKQIG-TFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIR
          GRPTSSQSYEQNIKQI..TFASVEQ.WR.YSH.V.PGDLTG..DFHLFK.GIKPMWEDDA.KN.G.WII.
Retrocopy GRPTSSQSYEQNIKQIT<TFASVEQLWRLYSHVVCPGDLTGQNDFHLFKKGIKPMWEDDADKNDG*WIIW

Parental  LRKGLASRCWENLILAMLGEQFMVGEEICGAVV-SVRFQEDIISIWNKTASDQATTARIRDTLRRVLNLP
          L.KG.AS.CWE.LILA.LG.QFMVGEE...AVV....FQEDI.S.WNKTAS.Q.TT..I.D.L.RVLNLP
Retrocopy L*KGVASHCWEKLILAILGYQFMVGEEVYVAVV<LI*FQEDILSTWNKTASNQVTTGQIWDMLWRVLNLP

Parental  PNTIMEYKTHTDSIKTPGRLGPQRLLFQNLWKPRLNVP
          PNTIM..KTHT.SIK.PGR.GPQRLLFQNLWKP.LNVP
Retrocopy PNTIMG*KTHTNSIKMPGRMGPQRLLFQNLWKPWLNVP

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_720 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,