RetrogeneDB ID: retro_pvam_293

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2383:28403..28863(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NMRK1
• Ensembl ID: ENSPVAG00000006121
• Aliases: None
• Description: nicotinamide riboside kinase 1 [Source:HGNC Symbol;Acc:26057]

Sequence

>retro_pvam_293
GATACAGATAAAAATGGATTTATGCAGTATGAGGTGCTTGAAGCACTTACCATGAAAAATAATGATGTCCACCATTTCTT
GCTGGATAGAAAGCCCCAAATGCTCTCTGATATCAACAGACTGGGGAAACACTGAGGAAATTCCCATATTAATCATCCAA
GGTTTCCTTTTGTTTAATTATAGGCCCCTTGATACTATATGGAATAGAAGCTACTTTCTGACGATTCCATATGAGGAACC
TAAGAGGAGAAGTAGTAGTAGTACAGGGGTCTGCAAGCCCTCAGATATCCTAGACTACTTCGATGGCCACATGTGGCCCA
TGTATCTAAAGCACAGAGGAGAAATGGAGGACATCATATGGGAAATTGTTTACCCAGATGGAGTAAAATCTGAAGAAAGC
CTCTTTTCACAAGTGTATGAATATCTAAGACAAGAACTAGCAAAGCAAAAATGTCAGCAG

Alignment

ORF - retro_pvam_293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.68 %
• Parental protein coverage: 74.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EIDENGFLQYDVLEALNMEK-MMSTISSWIESPSHSPVSTDQGNAEEIPILIIEGFLLFNYKPLDTIWNR
          ..D.NGF.QY.VLEAL.M...MMSTIS.WIESP..S..STD.GN.EEIPILII.GFLLFNY.PLDTIWNR
Retrocopy DTDKNGFMQYEVLEALTMKN>MMSTISCWIESPKCSLISTDWGNTEEIPILIIQGFLLFNYRPLDTIWNR

Parental  SYFLTIPYEECKKR--RSTRVYKPPDPPGYFDGHVWPMYLKHRREMEDITSEIVYLDGTKSEEELFSQVY
          SYFLTIPYEE.K.R...ST.V.KP.D...YFDGH.WPMYLKHR.EMEDI..EIVY.DG.KSEE.LFSQVY
Retrocopy SYFLTIPYEEPKRRSSSSTGVCKPSDILDYFDGHMWPMYLKHRGEMEDIIWEIVYPDGVKSEESLFSQVY

Parental  EDLRQELAKRKCLQ
          E.LRQELAK.KC.Q
Retrocopy EYLRQELAKQKCQQ

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_293 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005312	1 retrocopy	retro_amel_664,
Felis catus	ENSFCAG00000028823	1 retrocopy	retro_fcat_1087,
Macropus eugenii	ENSMEUG00000009787	1 retrocopy	retro_meug_275,
Mustela putorius furo	ENSMPUG00000012337	1 retrocopy	retro_mputfur_634,
Pteropus vampyrus	ENSPVAG00000006121	1 retrocopy	retro_pvam_293 ,
Tupaia belangeri	ENSTBEG00000004063	2 retrocopies	retro_tbel_1021, retro_tbel_4275,
Tarsius syrichta	ENSTSYG00000004232	1 retrocopy	retro_tsyr_718,