RetrogeneDB ID: retro_pvam_550

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3693:63601..64225(-)
• Located in intron of: ENSPVAG00000011223

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSMO1
• Ensembl ID: ENSPVAG00000013707
• Aliases: None
• Description: methylsterol monooxygenase 1 [Source:HGNC Symbol;Acc:10545]

Sequence

>retro_pvam_550
AGTGTCAGCATCTTCATTTCAGTATCCCTGGCTGTGGAATATGTAGATTCACTTTTACCTGAGAATTCTCTGCAAGAACC
ATTTAAAAATGCTTGGAACTATACGTTAGATAATTATACAATATCCCAGATTGCAACATGGGGATCTCTAGTAGTTCATG
AAGCCCTTTATTTCTTGTTCTGTTTACCTGGATTTTTGTTTCAATTTATACCTTACATGAAAAAGGTACAAAATTCAAAA
GGATAAACTAGAAACATGGGAAAAACAATGGCAATACCTTAAAGTACTTCTCTTTAATCACTTTTGTATCCAGCTTCCTT
TGATTTGTGGAACTTATTATTTTACAGAGTATTTCAATTCCTTATGATTGGGAAAGAATGCCAACATGGTATATGCTCTG
GACAGGATGGTTTGGTTATGAGATAATTAAGGATACCTGGCACTATTTCCTAAATAGGCTCTTCTTACACAACAAAAATA
TATAAGTGTATTCATAAAACTCATCATGAGTTTCAGGCTACATTTGGAACGGAAGCTGAATATACACGTCTCTTGGAAAC
ACTAATTCTTGGTACTGGGTTTTTCATTGGAATCATGCTTTTATGTGATTACATAGTCTTTTTG

Alignment

ORF - retro_pvam_550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.99 %
• Parental protein coverage: 70.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NVSIFSSASLAVEYVDSLLPENPLQEPFKNAWNYMLDNYTKFQIATWGSLIIHEVIYFLFSLPGFLFQFI
          .VSIF.S.SLAVEYVDSLLPEN.LQEPFKNAWNY.LDNYT..QIATWGSL..HE..YFLF.LPGFLFQFI
Retrocopy SVSIFISVSLAVEYVDSLLPENSLQEPFKNAWNYTLDNYTISQIATWGSLVVHEALYFLFCLPGFLFQFI

Parental  PYMKK-YKIQKDKPETWEGQWKCFKVLLFNHFCIQFPLICGTYYF-TEYFNIPYDWETMPRWYLLLARCF
          PYMKK.YKIQKDK.ETWE.QW...KVLLFNHFCIQ.PLICGT.Y.......IPYDWE.MP.WY.L....F
Retrocopy PYMKK>YKIQKDKLETWEKQWQYLKVLLFNHFCIQLPLICGT-YY>LQSISIPYDWERMPTWYMLWTGWF

Parental  GCAVIEDTWHYFLHRLLHHK-RIYKYIHKIHHEFQAP-GMEAEYAHPLETLILGTGFFMGIILLCDHVVL
          G...I.DTWHYFL.RL..H...IYK.IHK.HHEFQA..G.EAEY...LETLILGTGFF.GI.LLCD..V.
Retrocopy GYEIIKDTWHYFLNRLFLHN>KIYKCIHKTHHEFQATFGTEAEYTRLLETLILGTGFFIGIMLLCDYIVF

Parental  L
          L
Retrocopy L

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_550 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 16 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005596	1 retrocopy	retro_amel_447,
Choloepus hoffmanni	ENSCHOG00000007550	2 retrocopies	retro_chof_1657, retro_chof_560,
Callithrix jacchus	ENSCJAG00000009301	1 retrocopy	retro_cjac_2245,
Felis catus	ENSFCAG00000023004	1 retrocopy	retro_fcat_863,
Homo sapiens	ENSG00000052802	1 retrocopy	retro_hsap_4672,
Gorilla gorilla	ENSGGOG00000015730	1 retrocopy	retro_ggor_2898,
Loxodonta africana	ENSLAFG00000007061	1 retrocopy	retro_lafr_570,
Macaca mulatta	ENSMMUG00000012994	1 retrocopy	retro_mmul_2486,
Nomascus leucogenys	ENSNLEG00000006501	1 retrocopy	retro_nleu_2164,
Oryctolagus cuniculus	ENSOCUG00000003769	1 retrocopy	retro_ocun_1454,
Otolemur garnettii	ENSOGAG00000009281	2 retrocopies	retro_ogar_182, retro_ogar_3404,
Pan troglodytes	ENSPTRG00000016574	1 retrocopy	retro_ptro_3104,
Pteropus vampyrus	ENSPVAG00000013707	4 retrocopies	retro_pvam_1405, retro_pvam_550 , retro_pvam_598, retro_pvam_784,
Sorex araneus	ENSSARG00000013546	1 retrocopy	retro_sara_635,
Sarcophilus harrisii	ENSSHAG00000000135	1 retrocopy	retro_shar_530,
Tursiops truncatus	ENSTTRG00000012897	2 retrocopies	retro_ttru_20, retro_ttru_801,