RetrogeneDB ID: retro_pvam_1417

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_8237:2250..3534(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000017012
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GK
• Ensembl ID: ENSPVAG00000012460
• Aliases: None
• Description: glycerol kinase [Source:HGNC Symbol;Acc:4289]

Sequence

>retro_pvam_1417
ATGGCAGCCCCGAAGGAATCAGTTGTGGGGCCGTTGGTGGGCGCAGTGGTCCAAGGGACTAACTCTTCTAGATTTCTGGT
TTTCAATTCAAAAACAGCAGAACTACTTAGTCACCATCAAGTACAATTAACACAAGAGTTTCCAAAAGAAGGATGGGTGG
AACAAGACCCTAAGGAAATTCTTCAGTCTGTCTATGAGTGTATAGAGAGAACGTGTGAGAAACTTAACGAAGTGAATATT
GATATATCCAACATAAAAGCTATTGGTGTCAGCAATCAGAGAGAAACCACTCTTATCTGGGACAAGTTAACTGGAGAGCC
GCTCTACAATGCTGTGGCGTGGCTGGATCTGAGAACCCAGTCTACAGTTGAGAATCTTAGTAAAAAAATTCCAGGAAATA
ATAACTTTGTAAAGTCCAAGACAGGCCTTCCACTTAGCACTTACTTCAGTGCAGTGAAACTTCGTTGGATTCTCGACAAT
GTGAGCGAAGTTCAGAAAGCCATTGAAGAAGATAGAGCTCTTTTTGGTACCATGGATTCATGGCTTATCTGGAATTTGAC
AGGAGGAGTTAATGAAGGTGTCCACTGTACAGATGTAACAAACGCAAGTAGGACAATGCTTTTCAACATTCATTCTTTGG
AATGGGATAAAGAGCTCTGTGACTTTTTTGAAATTCCCATGAGCATTCTCCCAAATGTCTGCAGTTCTTCTGAGATCTAT
GGCTTAATGAAAGCTGGAGCCTTAGAAGGTGTGCCAATATCTGGGTGTTTGGGGGACCAGTCTGCTGCATTAGTGGGGCA
AATGTGCTTCCAGGAAGGACAAGCCAAAAATACATATGGAACAGGTTGTTTCTTACTATGTAATACCGGCCGTAAGTGTG
TATTTTCTGAACATGGCCTTCTGACCACAGTGGCTTACAAATTAGGCAGAGAAAAGCCAGCATTTTATGCACTGGAGGGT
TCTGTTGCTATAGCAGGTGCCGTTATTCGCTGGCTAAAAGACAATCTTGGAATTATAGAAACCTCAGAAGAAGTTGAAAA
ACTTGCTGAAGAAGCAGGTACTTCCTATGGCTGCTACTTCATCCCAGCCTTTTCAGGGTTATATGCACCTTATTGGGATC
CCAGTGCAAGAGGGATAATCTGTGGTCTCACTCAGTTCACCAATAAAAGCCATATTGCTTTCGCTGCATTAGAAGCTATT
TGTTTCCAAACCCGAGAGATAGTGGATTCCATGAACCGTGACTGTGAATTCATCAGTCATTTGCAGGTAGATGGAAAAAT
GACA

Alignment

ORF - retro_pvam_1417 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.48 %
• Parental protein coverage: 77.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPMEILQSVYECIEK
          MAA.K..V.GPLVGAV.QGT.S.RFLVFNSKTAELLSHHQV...QEFP.EGWVEQDP.EILQSVYECIE.
Retrocopy MAAPKESVVGPLVGAVVQGTNSSRFLVFNSKTAELLSHHQVQLTQEFPKEGWVEQDPKEILQSVYECIER

Parental  TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVEILSKRIPGNNNFVKSK
          TCEKL...NIDISNIKAIGVSNQRETT..WDKLTGEPLYNAV.WLDLRTQSTVE.LSK.IPGNNNFVKSK
Retrocopy TCEKLNEVNIDISNIKAIGVSNQRETTLIWDKLTGEPLYNAVAWLDLRTQSTVENLSKKIPGNNNFVKSK

Parental  TGLPLSTYFSAVKLRWLLDNVTKVQKAVKEDRALFGTIDSWLIWSLTGGANGGVHCTDVTNASRTMLFNI
          TGLPLSTYFSAVKLRW.LDNV..VQKA..EDRALFGT.DSWLIW.LTGG.N.GVHCTDVTNASRTMLFNI
Retrocopy TGLPLSTYFSAVKLRWILDNVSEVQKAIEEDRALFGTMDSWLIWNLTGGVNEGVHCTDVTNASRTMLFNI

Parental  HSLEWDKDLCEFFDIPMKILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
          HSLEWDK.LC.FF.IPM.ILPNV.SSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQ.GQAKNTYG
Retrocopy HSLEWDKELCDFFEIPMSILPNVCSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQEGQAKNTYG

Parental  TGCFLLCNTGRKCVFSDHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKTSEEIEKLAK
          TGCFLLCNTGRKCVFS.HGLLTTVAYKLGR.KP..YALEGSVAIAGAVIRWL.DNLGII.TSEE.EKLA.
Retrocopy TGCFLLCNTGRKCVFSEHGLLTTVAYKLGREKPAFYALEGSVAIAGAVIRWLKDNLGIIETSEEVEKLAE

Parental  EVGTSYGCYFVPAFSGLYAPY-EPSARGIICGLTQFTNKCHVAFAALEAVCFQTREILDAMNRDCGIPLS
          E.GTSYGCYF.PAFSGLYAPY..PSARGIICGLTQFTNK.H.AFAALEA.CFQTREI.D.MNRDC....S
Retrocopy EAGTSYGCYFIPAFSGLYAPYWDPSARGIICGLTQFTNKSHIAFAALEAICFQTREIVDSMNRDCEF-IS

Parental  HLQVDGGMT
          HLQVDG.MT
Retrocopy HLQVDGKMT

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_1417 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003261	2 retrocopies	retro_cpor_11, retro_cpor_20,
Felis catus	ENSFCAG00000004264	1 retrocopy	retro_fcat_140,
Monodelphis domestica	ENSMODG00000002417	1 retrocopy	retro_mdom_234,
Oryctolagus cuniculus	ENSOCUG00000013023	2 retrocopies	retro_ocun_2, retro_ocun_81,
Pteropus vampyrus	ENSPVAG00000012460	1 retrocopy	retro_pvam_1417 ,
Sarcophilus harrisii	ENSSHAG00000006470	1 retrocopy	retro_shar_35,
Sus scrofa	ENSSSCG00000012202	2 retrocopies	retro_sscr_479, retro_sscr_59,