RetrogeneDB ID: retro_pvam_13

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_5572:29685..31842(+)
• Located in intron of: ENSPVAG00000013059

Retrocopy information

• Ensembl ID: ENSPVAG00000013061
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC5A2
• Ensembl ID: ENSPVAG00000012531
• Aliases: None
• Description: solute carrier family 5 (sodium/glucose cotransporter), member 2 [Source:HGNC Symbol;Acc:11037]

Sequence

>retro_pvam_13
ATGAGGGCTGTACTGGAGACAGCAGACATTGCCATAGTGGCCCTGTATTTTATCCTGGTCATGTGCATTGGTTTTTTTGC
CATGTGGAAATCTAATAGAAGCACCGTGAGTGGATACTTCCTGGCTGGGCGCTCTATGACCTGGGTGGCGATTGGTGCCT
CTCTGTTTGTGAGCAATATTGGGAGTGAGCACTTCATTGGGCTAGCGGGATCTGGAGCTGCAAGTGGATTTGCAGTAGGC
GCATGGGAATTCAATGCCTTACTGCTTTTGCAACTTCTGGGATGGGTTTTTATCCCGATTTACATCCGGTCAGGGGTATA
CACCATGCCTGAATACTTGTCCAAGCGATTTGGTGGCCATAGGATTCAGGTCTATTTTGCGGCCTTGTCTTTAATTCTTT
ATATCTTCACCAAGCTTTCAGTGGATCTGTATTCGGGTGCCCTCTTTATCCAGGAGTCTTTGGGTTGGAACCTATATGTG
TCTGTCATCCTGCTCATTGGCATGACTGCTTTGCTGACTGTCACCGGAGGCCTTGTTGCAGTAATCTACACAGACACTCT
CCAGGCTCTGCTCATGATCGTTGGGGCACTCACACTTATGATTATTAGCATGATGGAGATTGGCGGGTTTGAGGAAGTTA
AGAGAAGGTACATGTTGGCCTCACCCAATGTCACTTCCATCTTGTTGACGTACAACCTTTCCAACACAAATTCTTGTAAT
GTCCACCCTCAGAAAGATGCACTGAAAATGTTGCGGAATCCAACAGATGAAGATGTTCCGTGGCCTGGATTCATTCTTGG
GCAGACCCCAGCTTCAGTTTGGTACTGGTGTGCTGACCAAGTCATCGTGCAGAGGGTACTCGCGGCTAAAAACATTGCGC
ATGCCAAAGGCTCTACTCTAATGGCTGGCTTCTTGAAGCTTTTGCCAATGTTTATCATAGTTGTCCCAGGAATGATTTCC
AGGATATTGTTTACTGATGATATAGCTTGCATCAACCCAGAGCACTGCATGCAAGTGTGTGGAAGCAGAGCTGGGTGCTC
TAATATTGCTTACCCACGCCTGGTGATGAAACTGGTTCCTGTGGGCCTCCGAGGCTTAATGATGGCAGTGATGATTGCAG
CTCTGATGAGTGACTTGGACTCTATCTTTAACAGTGCCAGTACCATATTCACCCTCGATGTGTACAAACTTATCCGCAAG
AGTGCAAGCTCCCGGGAACTAATGATTGTGGGGAGGATATTCGTGGCTTTTATGGTGGTGATCAGCATCGCGTGGGTGCC
AATCATCGTGGAGATGCAAGGAGGCCAGATGTACCTTTATATTCAGGAGGTAGCAGATTACCTGACGCCCCCAGTCGCGG
CCCTGTTCCTTCTGGCAATTTTCTGGAAACGCTGCAATGAACAAGGGGCTTTCTATGGTGGAATGGCTGGCTTTGTTCTT
GGAGCAGTTCGTTTGACACTGGCCTTTGCCTACCGTGCCCCAGAATGTGACCAACCTGATAACAGGCCAGACTTCATCAA
AGACATTCATTACATGTATGTGGCCACAGCATTGTTTTGGGTCACAGGACTCATTACTGTAATCGTTAGCCTTCTCACTC
CACCTCCCACGAAGGAACAGATTCGTACTACCACCTTTTGGTCTAAGAAGAGCCTGGTGGTGAAGGAGAGCTGCTCCCCA
AAAGACGAACCATACAAAATGCAAGAGAAGAGCATTCTGAGATGCAGCGAGAATAGCGAGGCCATCAACCACATCATTCC
CAATGGGAAATCTGAAGATAGCATTAAGGGCCTTCAGCCTGAAGATGTTAATCTCTTGGTGACCTGCAGAGAGGAGGGCA
ACCCAGTGGCCTCCTTAGGTCATTCAGAGGCAGAAACACCAGTAGATGCTTATTCCAATGGGCAAGCAGCGCTCATGGGT
GAGAAAGAGAGAAAGAAGGAAACAGAAGATGGAGGCCGGTATTGGAAGTTCATAGATTGGTTCTGTGGCTTTAAAAGTAA
GAGCCTCAGCAAGAGGAGTCTCAGAGACCTGATGGAGGAGGAGGCTGTTTGTTTACAAATGTTGGAAGAGCCTCCGCAAG
TTAAACTAATACTGAATATTGGACTTTTTGCTGTGTGTTCACTTGGAATTTTCATGTTTGTTTATTTCTCCTTATGA

Alignment

ORF - retro_pvam_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.09 %
• Parental protein coverage: 81.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADILVIAAYFLLVIGVGLWSMRRTNRGTVGGYFLAGRSMVWWPVGASLFASNIGSGHFVGLAGTGAASGL
          ADI...A.YF.LV...G...M...NR.TV.GYFLAGRSM.W...GASLF.SNIGS.HF.GLAG.GAASG.
Retrocopy ADIAIVALYFILVMCIGFFAMWKSNRSTVSGYFLAGRSMTWVAIGASLFVSNIGSEHFIGLAGSGAASGF

Parental  AVAGFEWNALFVVLLLGWLFAPVYLTAGVITMPQYLRKRFGGHRIRLYLSVLSLFLYIFTKISVDMFSGA
          AV...E.NAL....LLGW.F.P.Y...GV.TMP.YL.KRFGGHRI..Y...LSL.LYIFTK.SVD..SGA
Retrocopy AVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGHRIQVYFAALSLILYIFTKLSVDLYSGA

Parental  VFIQQALGWNIYASVIALLGITMIYTVTGGLAALMYTDTVQTFVILGGAFILMGYGFHEVGGYSGLFDKY
          .FIQ..LGWN.Y.SVI.L.G.T...TVTGGL.A..YTDT.Q......GA..LM.....E.GG.......Y
Retrocopy LFIQESLGWNLYVSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIVGALTLMIISMMEIGGFEEVKRRY

Parental  LGAMTSL-TVSEDPAVGNISSSCYQPRPDSYHLLRDPVTGDLPWPALLLGLTIVSGWYWCSDQVIVQRCL
          ..A..............N..S....P..D....LR.P...D.PWP...LG.T..S.WYWC.DQVIVQR.L
Retrocopy MLASPNVTSILLTYNLSNTNSCNVHPQKDALKMLRNPTDEDVPWPGFILGQTPASVWYWCADQVIVQRVL

Parental  AGKSLTHIKAGCILCGYLKLMPMFLMVMPGMISRILYPDEVACVVPEVCKRVCGTEVGCSNIAYPRLVVK
          A.K...H.K......G.LKL.PMF..V.PGMISRIL..D..AC..PE.C..VCG...GCSNIAYPRLV.K
Retrocopy AAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFTDDIACINPEHCMQVCGSRAGCSNIAYPRLVMK

Parental  LMPNGLRGLMLAVMLAALMSSLASIFNSSSTLFTMDIYTRLRPRASDRELLLVGRIWVVFIVAVSVAWLP
          L.P.GLRGLM.AVM.AALMS.L.SIFNS.ST.FT.D.Y...R..AS.REL..VGRI.V.F.V..S.AW.P
Retrocopy LVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKSASSRELMIVGRIFVAFMVVISIAWVP

Parental  VVQAAQGGQLFDYMQAVSSYLAPPVSAVFVLALFVPRVNEKGAFWGLIGGLLMGLARLIPEFSFGSGSCV
          .....QGGQ...Y.Q.V..YL.PPV.A.F.LA.F..R.NE.GAF.G...G...G..RL...F......C.
Retrocopy IIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFVLGAVRLTLAFAYRAPECD

Parental  RPSACPALLCGVHYLYFAIVLFVCSGLLTLVVSLCTAPIPRKHLHRLVFSLRHSKEERE
          .P...P......HY.Y.A..LF...GL.T..VSL.T.P..........F....S....E
Retrocopy QPDNRPDFIKDIHYMYVATALFWVTGLITVIVSLLTPPPTKEQIRTTTFWSKKSLVVKE

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_13 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011926	1 retrocopy	retro_acar_109,
Ailuropoda melanoleuca	ENSAMEG00000016218	1 retrocopy	retro_amel_32,
Bos taurus	ENSBTAG00000010096	1 retrocopy	retro_btau_287,
Canis familiaris	ENSCAFG00000016909	1 retrocopy	retro_cfam_157,
Felis catus	ENSFCAG00000001380	1 retrocopy	retro_fcat_110,
Latimeria chalumnae	ENSLACG00000007334	1 retrocopy	retro_lcha_35,
Loxodonta africana	ENSLAFG00000005737	1 retrocopy	retro_lafr_54,
Myotis lucifugus	ENSMLUG00000011500	1 retrocopy	retro_mluc_218,
Mus musculus	ENSMUSG00000030781	1 retrocopy	retro_mmus_200,
Pteropus vampyrus	ENSPVAG00000012531	1 retrocopy	retro_pvam_13 ,
Tursiops truncatus	ENSTTRG00000012500	1 retrocopy	retro_ttru_2,