RetrogeneDB ID: retro_pvam_1125

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_31222:2566..4141(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FANCB
• Ensembl ID: ENSPVAG00000000827
• Aliases: None
• Description: Fanconi anemia, complementation group B [Source:HGNC Symbol;Acc:3583]

Sequence

>retro_pvam_1125
ATGACGAGCAAACAAGCAATGTTATCTAATAAACAAGAAAGGCTCATGTGTTATAATGGGGAAGTTCTTGTTTTTCGATT
GTCTAAAGGAAATTTTGCAGATAAAGGGCCTGCAGAAATACCCATATTACATGTCAGAAGAATGGTATTTGACAGAGGAA
CAAGAACATTTGTTCAGAAGTCTACTGGATTCTTTAACATAAAGGAAGAAAACTCTTATTTAAAAATTATGTGTTGCGAC
TGTGTGTCAGATTTCAGAACTGGGATGAACCTCCTTTGTATTGTTATACAATGCAATGAAAAGAGTGATGTTTTCAAATA
TTTTCTACTGTTTCTTCACAGTACCAATAAATTTGAAAAGTGTTTGAGTTTTAGACTAGGCCATGAGTTGAAGGATGGCA
TAAGGGTCTTTAATGGCCCTTTAATTTTATGGAAACATGTCAAAACATTCTTTTATATCTCTTCCCAAGCTGGCAATGTT
ATTACTGTGTCCATCAACTTTTCCTCTATTGAGTGGGCAGGGGAGATTGAAAATCTAGGTATGGTTTTATTAAGACAAAA
GAAATATTATTTATCTGAGGAAGAATGTACCCCAAAGCTTTCAAAATCAGATTATGCATTTTGAAATACCAAGTTTTGCA
TATACTCCCTTGAAAGTGAAGAAGTAATTAGCAATACATACATTATCCCTCCTGCTTACAGCAGTGTGATAACTTGTGTG
CATGTCTGTGCAACCGAGATTGTTGTCAACAACCAGCTAAGAATGTCTCTGATTGCCCTTACTGAAAAGGATCAGCTGAT
TTCGTTCCAAAATGGGACTCCTAAAAGTGTGTGCCAGCTTCCATGTGGAGGTCCTTGTGCACTTCAACTTATGGATTCGG
GTGGAGACCTCCTTTTCCTTGTATCTTTTAGGTTCAGTGATGCTTGTGCTGTTTGGGAAAAGAACTTTCAGGTTGCTGCT
AAATGGGAAAAAATTAGCTTAGTACTGATAGATGGAACTGGAAATGAACAAGTACTGCTACTTTTTCAGGACTCCTTAAA
TTCAGATTGCCTGAGTTCATTTAAAATAACAGATCTTGACAACATACACTATTCAAGTGAAACACTGGATTGCAATGAAG
ATGACTTATTTGAGGACAAACAAGATCATCGTTATTTGGTGATTCCAGCTCTGGAAAGGAGAGTGAAAGTTGGATTAACT
TCTATTCGGGAAGTACAGCAGCATCTCTTGCTTAAGGAAAAATTTATTTTAAAATCTTACAAAGCTTTAGTGAACCTGGT
TCAAGGGAAAGAAGATAGTACATCAAGTGCAGAGGTGGAATGTCTTGTTACTCTTTGTGGTAAAGAAGAAAATCCTGTCC
AAACTTTTGATGAAAAATCATCAGACAATTCTCAAGGTTCAGAACAGCTAGTAGAGAACGTACGATATCGTGTAATAGAT
GACAGCTTGGTTGTTGGAGTGAACAGCACATCTTCGAAACTGTCCCTGAACTGGGTGACTTTATTGTAGTTAATGGATCA
ACTCCATAGCTTCAGCTGTCCTCTTACTAAGTGTCAGAGTGATCAAGTTGAGTCG

Alignment

ORF - retro_pvam_1125 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 61.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTSKQAMSSKEQERLLCYNGEVLVFRLSKGSFSHKGPAEIPVLHVRRMVFDRGTRTFVQKSTGFFSIKEE
          MTSKQAM.S..QERL.CYNGEVLVFRLSKG.F..KGPAEIP.LHVRRMVFDRGTRTFVQKSTGFF.IKEE
Retrocopy MTSKQAMLSNKQERLMCYNGEVLVFRLSKGNFADKGPAEIPILHVRRMVFDRGTRTFVQKSTGFFNIKEE

Parental  NSYLKILCCDCVSDFRTRMNLPCIVIQCNEKNNVFKYFLLFLHSTNKFEKRLSFRL-HEL-DGIRVFN-P
          NSYLKI.CCDCVSDFRT.MNL.CIVIQCNEK..VFKYFLLFLHSTNKFEK.LSFRL.HEL.DGIRVFN.P
Retrocopy NSYLKIMCCDCVSDFRTGMNLLCIVIQCNEKSDVFKYFLLFLHSTNKFEKCLSFRLGHELKDGIRVFNGP

Parental  LILWKHV--FFYISSQTDKVITLSFYFLLV--VGEIGNLG--VLGQKK-CLSEEECTPKPSKSDYAFWNT
          LILWKHV..FFYISSQ...VIT.S..F......GEI.NLG...L.QKK..LSEEECTPK.SKSDYAF.NT
Retrocopy LILWKHVKTFFYISSQAGNVITVSINFSSIEWAGEIENLGMVLLRQKKYYLSEEECTPKLSKSDYAF*NT

Parental  KFCVYSLESEELISDTYIIPPAYSSVITCVHVCATEI-VNSQLRMSLIALTRKDQLISFQNGTPKSVCQL
          KFC.YSLESEE.IS.TYIIPPAYSSVITCVHVCATEI.VN.QLRMSLIALT.KDQLISFQNGTPKSVCQL
Retrocopy KFCIYSLESEEVISNTYIIPPAYSSVITCVHVCATEIVVNNQLRMSLIALTEKDQLISFQNGTPKSVCQL

Parental  PFADPRAVQLMDSGGDLFFLVSFRSSEVCAVWEKNFQVAAKWEKISSVLIDDFIGTGTDQVLLLFKDSLD
          P...P.A.QLMDSGGDL.FLVSFR.S..CAVWEKNFQVAAKWEKIS.VLID...GTG..QVLLLF.DSL.
Retrocopy PCGGPCALQLMDSGGDLLFLVSFRFSDACAVWEKNFQVAAKWEKISLVLID---GTGNEQVLLLFQDSLN

Parental  SDCLSSFKITDLDNMNYSSETPDCNEDDLFEDKQDK---LVPALERRVKVGLASIQELQQHLLLKEKIIL
          SDCLSSFKITDLDN..YSSET.DCNEDDLFEDKQD......PALERRVKVGL.SI.E.QQHLLLKEK.IL
Retrocopy SDCLSSFKITDLDNIHYSSETLDCNEDDLFEDKQDHRYLVIPALERRVKVGLTSIREVQQHLLLKEKFIL

Parental  KSSKAFMNLVQGKEDSTSSAEEKECLVTLCGKEENPVHTFDEKIPDNSQGSEQLVEKIWYRVIDDSLVVG
          KS.KA..NLVQGKEDSTSSA.E.ECLVTLCGKEENPV.TFDEK..DNSQGSEQLVE...YRVIDDSLVVG
Retrocopy KSYKALVNLVQGKEDSTSSA-EVECLVTLCGKEENPVQTFDEKSSDNSQGSEQLVENVRYRVIDDSLVVG

Parental  VKTTSSSKLALNRVTLSLLMDQPQSSCSPLIKCQNRVIKS
          V..T.SSKL.LN.VTL..LMDQ..S...PL.KCQ.....S
Retrocopy VNST-SSKLSLNWVTLL*LMDQLHSFSCPLTKCQSDQVES

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_1125 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000008747	1 retrocopy	retro_ogar_216,
Pteropus vampyrus	ENSPVAG00000000827	1 retrocopy	retro_pvam_1125 ,