RetrogeneDB ID: retro_pvam_1404

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_8009:6170..6824(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMX2
• Ensembl ID: ENSPVAG00000004425
• Aliases: None
• Description: RNA binding motif protein, X-linked 2 [Source:HGNC Symbol;Acc:24282]

Sequence

>retro_pvam_1404
CTTACAAAGATGAACCCATTAACCAAAGTGAAGCTGGTTAGTGAGCTGAATGAACGGGAGGCCCATATTGCCGTGGCAGC
TACGGCGTCATGGCACTCTGAGTACAAGGACAGCGCCTGGATCTTCGTGGGAGGGCTTCCTTTTGAACTGACCGAAGGAG
ATATCCTCTGTGTATTCTCTCAGTATGGAGAGATTGTTAACATTAATCTCGTGCGAGACCAGAAGACAGGGAAGTCCAAA
GGATTCTGTTTTATCTGCTATGAAGACCAGAGGAGTACAGTTTTGGCCGTTGACAATTTTAATGGAATCAAGATCAAGGG
AAGAACTATCCGAGTCGACCATGTATCCTGCTACCGCCCCCCTCGGGTCCTAGAGGGCGTGGATGACGCCACCAGAAAGC
TGTGGCAGAAAGGCTGTGGGATTCAGACCTCCTCATCGAGCTCATCTGAAGGCTCCGAAGACGAAGCACTCTCCGAACAC
CATAAACAAGAGAAACAGAAAAGAAGTAAGACCAAAGAGAGGACTACTATACTAGTTAAAGACGAGGAGAGACAGACACA
GCAGCCATTGTTCCTGGCAGCGAGAGGCCAGATTAAGATGGAAGACACCCTAGGTTCCGATGAACGTGCCAAGGTGAAGT
TTGAGTCTAGAGAG

Alignment

ORF - retro_pvam_1404 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.09 %
• Parental protein coverage: 64.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAGMNPLTKVKLINELNEREVQLGVADKVSWHSEYKDSAWIFLGGLPYELTEGDIICVFSQYGEIVNINL
          L..MNPLTKVKL..ELNERE....VA...SWHSEYKDSAWIF.GGLP.ELTEGDI.CVFSQYGEIVNINL
Retrocopy LTKMNPLTKVKLVSELNEREAHIAVAATASWHSEYKDSAWIFVGGLPFELTEGDILCVFSQYGEIVNINL

Parental  VRDKKTGKSKGFCFLCYEDQRSTILAVDNFNGIKIKGRTIRVDHVSNYRAPKDSEEMDDVTRELQDEGCG
          VRD.KTGKSKGFCF.CYEDQRST.LAVDNFNGIKIKGRTIRVDHVS.YR.P...E..DD.TR.L...GCG
Retrocopy VRDQKTGKSKGFCFICYEDQRSTVLAVDNFNGIKIKGRTIRVDHVSCYRPPRVLEGVDDATRKLWQKGCG

Parental  AHTTLPNSSEGSEDDKPTKKHKKDKKERKKRKKDKEKTDREVQAEQPASFSFPRSKMIKEKDDSGSKKHS
          ..T....SSEGSED......HK..K..R.K.K.........................IK..D..GS....
Retrocopy IQTSSSSSSEGSEDEALSEHHKQEKQKRSKTKERTTILVKDEERQTQQPLFLAARGQIKMEDTLGSDERA

Parental  SKNSERHQ
          ....E...
Retrocopy KVKFESRE

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_1404 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000017095	1 retrocopy	retro_mluc_310,
Oryctolagus cuniculus	ENSOCUG00000011809	1 retrocopy	retro_ocun_106,
Pteropus vampyrus	ENSPVAG00000004425	1 retrocopy	retro_pvam_1404 ,
Sarcophilus harrisii	ENSSHAG00000016412	1 retrocopy	retro_shar_2,
Tursiops truncatus	ENSTTRG00000016210	1 retrocopy	retro_ttru_1561,