RetrogeneDB ID: retro_pvam_742

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_10439:15109..15814(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFR1
• Ensembl ID: ENSPVAG00000004202
• Aliases: None
• Description: SWI5-dependent recombination repair 1 [Source:HGNC Symbol;Acc:29574]

Sequence

>retro_pvam_742
GAGGTAAACCAAGATTCCATTTTCAAGATAAAAAGTCCTTCAGGCTCAACTTTAATTTTACCTAGCACTCCACAAGCCTG
TGCCAACCCACCATCTCCCCATACAAATTGTTCAAGTAAACAATCTGTGAGTGAAACGTTTAAAGAATGGTTAAGCGAAA
GTAGGTATTCATTCAATTCCTGTTATAGTGTGGTAAAATGTCTTAAAGTAGAGAATGATGAAATTGATCAGACCTTTTCA
GAGAAACCAGCGTCTTCAACAGAAGAAAACTGTTTGGAATTTCAAGAAAATTTTAAACACATAGACAGTGAATTTGAAGA
AAGTACATATCTGAAAAATACCTTCAAGAATATCAGTGCAAGTGGATCTAAATCACGTGATACTGGGTCTTGCAGTGATT
TCCATAATGACTATGTGAATGAGAATCTTCCCAAACAAAGATTAAATGAAGAAAAAGCAAAAATGATGAAGTAGATTCAC
GAGAAAGAAGACCTTTTTCAGAGGCTAAAACTAGTCAATATGTATAGATCTAAGAATTACCTGTCCCAGTTACATTTGTT
AATAAAGATGGGGAGAAGCTGTAGCCAGCTGTTGCTTTGTGAGTTGCAATCAGCTATGTCAGAGGAGAATAAGAAACTCA
GCCTTACTCAGTTGATAGACTACTATGGGTTAGATGATAAATTGCTACTGTATTACAGACATGAA

Alignment

ORF - retro_pvam_742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.04 %
• Parental protein coverage: 78.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVNQDFIFKMESSSDSAVILPSTPLACANPPSPHTSSSRKQPMSATLRERLRKTRSSFNSYYSVVKRLKI
          EVNQD.IFK..S.S.S..ILPSTP.ACANPPSPHT..S.KQ..S.T..E.L...R.SFNS.YSVVK.LK.
Retrocopy EVNQDSIFKIKSPSGSTLILPSTPQACANPPSPHTNCSSKQSVSETFKEWLSESRYSFNSCYSVVKCLKV

Parental  DSDENDQTFSEKPASSTKENCLEFQENFKHIDSEFEESTCLKNTFKNISTNESKSLDAESCSGLSNDCMN
          ..DE.DQTFSEKPASST.ENCLEFQENFKHIDSEFEEST.LKNTFKNIS...SKS.D..SCS...ND..N
Retrocopy ENDEIDQTFSEKPASSTEENCLEFQENFKHIDSEFEESTYLKNTFKNISASGSKSRDTGSCSDFHNDYVN

Parental  ESLPKQGLNEEKAKLVKQIQEKEDLLRRLKLVKMYRSKNDLSQLQLLIKKWRSCSQLLLCELQSAMSE--
          E.LPKQ.LNEEKAK..K.I.EKEDL..RLKLV.MYRSKN.LSQL.LLIK..RSCSQLLLCELQSAMSE..
Retrocopy ENLPKQRLNEEKAKMMK*IHEKEDLFQRLKLVNMYRSKNYLSQLHLLIKMGRSCSQLLLCELQSAMSEEN

Parental  NKLSLTQLI-HYGLDD-LLLYNRNE
          .KLSLTQLI..YGLDD.LLLY.R.E
Retrocopy KKLSLTQLIDYYGLDDKLLLYYRHE

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_742 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000005386	2 retrocopies	retro_ecab_726, retro_ecab_887,
Echinops telfairi	ENSETEG00000015444	1 retrocopy	retro_etel_1418,
Gorilla gorilla	ENSGGOG00000025713	1 retrocopy	retro_ggor_3039,
Macaca mulatta	ENSMMUG00000015327	1 retrocopy	retro_mmul_2606,
Pteropus vampyrus	ENSPVAG00000004202	1 retrocopy	retro_pvam_742 ,