RetrogeneDB ID: retro_pvam_1235

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_4636:12751..13534(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIH1D2
• Ensembl ID: ENSPVAG00000009619
• Aliases: None
• Description: PIH1 domain containing 2 [Source:HGNC Symbol;Acc:25210]

Sequence

>retro_pvam_1235
ATGAAATCATCCTCAAAAGGTCCACTCATGCGAGTTACTCAATTCTGGAATGTCCTAAATGACCTGTCTCAAAATCACCC
TGAGAGTTATGAGAAGTTCATTCGACAGCAGCTAAAAGAAAAGAAACAGCTCTGTGCTGCCCCAGAACCACAGATCTGTC
TGCAAACCAGAATTTTGAAACCAAAAGAAAAAATACTTTTTATCAACCTATGTCGGTGGAAAAGGATTCCAGCCTCCTAA
TCAACCATTCATTTAGGACCTCTAAGTGCTGGCAGACTAGAAATGTCTGAGACATCAGATGTTTACACAATCATCAATGT
TGCCTACAATCCTGATGTTTTCCAGGCAGCAGAAAAGGACCATAGGAAAAAAGATCAATTAGTAAGGATGGCTATGAAAT
GCCTTGAGAAACAACTCCAATTTACTCTCTCACATTTTTACCATATTACCAAATTTAAAATAAAAGGAAACATTCAAACG
ATGAGACAAAATCTGATGGTAATTCAAATTGACTCCACAGACTTAAGAGAGAAAACAAGAAAGGAACTAACTCATGAATA
GATACGAAATGGTACTGGATTATGCAATCCAGATCACTTCCCTCAACTTTTACTGCCAAAAGACCACTTTTCAGGCCAAA
CAGGGTGCCTGATAGAAGAGATTTCCAGTAAAGATATCCAGGTGGAGATGAAGAGACTAACCTATGAATTAAAAATTGTG
GTAGATTAGAATGAGAAAGCCCTGGAAATTGAATTAAAAATTGAATTACCAGGTATTAATTCA

Alignment

ORF - retro_pvam_1235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.05 %
• Parental protein coverage: 82.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESSSKGLLTQVTQFWNLLDDLAESNPESYEKFIAQQLKEGKQLCAAPEPQLCLQTRILKPKEKILFINL
          M.SSSKG.L..VTQFWN.L.DL....PESYEKFI.QQLKE.KQLCAAPEPQ.CLQTRILKPKEKILFINL
Retrocopy MKSSSKGPLMRVTQFWNVLNDLSQNHPESYEKFIRQQLKEKKQLCAAPEPQICLQTRILKPKEKILFINL

Parental  CQWKRIPAPQSTTHPVPLSVGRPEDMSETSDVYTVIDVAYNPDILQAAEDQVKK--QLIRMVMKCIEEQF
          C.WKRIPA..ST.H..PLS.GR.E.MSETSDVYT.I.VAYNPD..QAAE....K..QL.RM.MKC.E.Q.
Retrocopy CRWKRIPAS*STIHLGPLSAGRLE-MSETSDVYTIINVAYNPDVFQAAEKDHRKKDQLVRMAMKCLEKQL

Parental  Q-TLSHFYH--TFKIKGSIQRMKQNLMGIHTDPTYLREKMRKELTLEQIRNST-VSNPDHFPHLLLPKDH
          Q.TLSHFYH...FKIKG.IQ.M.QNLM.I..D.T.LREK.RKELT.E.IRN.T...NPDHFP.LLLPKDH
Retrocopy QFTLSHFYHITKFKIKGNIQTMRQNLMVIQIDSTDLREKTRKELTHE*IRNGTGLCNPDHFPQLLLPKDH

Parental  VSGQTSCLIEEISSKEIQVEMKRPAYELKIVTDQKEKPLKIELKVELPGINS
          .SGQT.CLIEEISSK.IQVEMKR..YELKIV.D..EK.L.IELK.ELPGINS
Retrocopy FSGQTGCLIEEISSKDIQVEMKRLTYELKIVVD*NEKALEIELKIELPGINS

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_1235 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004081	1 retrocopy	retro_amel_444,
Felis catus	ENSFCAG00000000608	1 retrocopy	retro_fcat_236,
Pteropus vampyrus	ENSPVAG00000009619	1 retrocopy	retro_pvam_1235 ,