RetrogeneDB ID: retro_pvam_340

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2636:301434..301814(+)
• Located in intron of: ENSPVAG00000015287

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_340
AACAAGTCTGACACACTGAAAGATGATGACAGTGGGAGCTATGATCAGAATGAATGAAATAGCGCACAGAAAGCTAGTAA
GAAGGAAAAAACGGAACGAGACTAGAGTCAGAGCAGCAGCAAGAGGAAGGCTGTTGTCCCTGGACCAGCAGAGCATCCCT
ACACTTTCCGGTCCTCCGGGAGAACCCCCAGCCGTCCCGCTGGCTCACAGAGCTATGAACAGACTATCAAACAGATTGGC
ACCTTTGCCTCTGTGGAGCAGTTCTGGAGGTTTCGCAGCTACATGGTACATCCTAGGGACCTGACAGGCCACAGTGACTC
CCATCTCTTCAAAGAAGGAATTTAAACCCATGTTGGGAGGATGATGCAAATGAAAATGGT

Alignment

ORF - retro_pvam_340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.52 %
• Parental protein coverage: 53.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NKFDALKDDDSGDHDQNEENSTQKDGEKEKMERDKSQSISKRKAVVPGPAEHPLQYNYTFWYSRRTPGRP
          NK.D.LKDDDSG..DQNE.NS.QK...KEK.ERD.SQS.SKRKAVVPGPAEHP....YTF..S.RTP.RP
Retrocopy NKSDTLKDDDSGSYDQNE*NSAQKASKKEKTERD*SQSSSKRKAVVPGPAEHP----YTFRSSGRTPSRP

Parental  TSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGI-KPM-WEDDANKNG
          ..SQSYEQ.IKQIGTFASVEQFWRF.S.MV.P.DLTGHSD.HLFKEGI.KPM.WEDDAN.NG
Retrocopy AGSQSYEQTIKQIGTFASVEQFWRFRSYMVHPRDLTGHSDSHLFKEGI>KPM>WEDDANENG

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_340 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,