RetrogeneDB ID: retro_pvam_34

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_108:162494..163054(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS2
• Ensembl ID: ENSPVAG00000016704
• Aliases: None
• Description: ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]

Sequence

>retro_pvam_34
CGCCTGGCCAAGGACAGAAAGGTCAGGTCTCTAGAGGAGACTTATCTCTTCTCTCTGCCCATCGAGGAACCTGAGACCTT
TGAATTTTTCTTGGGAGGCGTCCCTCAAGGACAAGGTTTTGAAGATTATGCCTATGCAAAATGGACCTTGGCTGGCCCAG
GTACCAGTATCAAGACACTTGTCACCATTGGGGATTATAATGGACATGCCTACCTTGGTGTAAGTGCTCCGAGGAGGTAG
CTGTGTCCATCTGTAGTGCCATCATCTTGGCCAAACTCTCCATCATCCCCATGAGGTGAGACTACTGGGGGAACAAGGTC
CACAAACCATAACTGTCCCTTGCAAGGTGACTGGCCTCTGTGACTCTCTGCTGGCATGCCTCATCCCTCTCTCTGGGGCA
CTGGCATCCTCCAGGTCTCTGTCCCCAAGAAGCTTCTGCTGATGGTGACACTGATGATTACTCCACCTCGGCAAGGGGCT
GTGCAGCCACCCTGGGCAGCCTTGCCAAGGTCACTTTGGATACTGTCTCCAAGATGTACAACTTTCTCATTCCTCATTTG

Alignment

ORF - retro_pvam_34 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.4 %
• Parental protein coverage: 64.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RLVKDMKIKSLEEIYLFSLPIKESEIIDFFLG-ASLKDEVLKIMPVQ-KQTRAGQRTRFKAFVAIGDYNG
          RL.KD.K..SLEE.YLFSLPI.E.E...FFLG.ASLKD.VLKIMP.Q.K.T.AG..T..K..V.IGDYNG
Retrocopy RLAKDRKVRSLEETYLFSLPIEEPETFEFFLG>ASLKDKVLKIMPMQ<KWTLAGPGTSIKTLVTIGDYNG

Parental  HVGLGV-KCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKP-HTVPCKVTGRCGSVLVRLIPAPR-GT
          H..LGV.KCS.EVA..I..AIILAKLSI.P.R..YWGNK..KP..TVPCKVTG.C.S.L..LIP....GT
Retrocopy HAYLGV<KCSEEVAVSICSAIILAKLSIIPMR*DYWGNKVHKP<ITVPCKVTGLCDSLLACLIPLSG<GT

Parental  GIVSAPVPKKLLMMAGI-DDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDL
          GI....VPKKLL.M....DD..TSARGC.ATLG..AK.T.D..SK.Y..L.P.L
Retrocopy GILQVSVPKKLLLMVTL<DDYSTSARGCAATLGSLAKVTLDTVSKMYNFLIPHL

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_34 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 9 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Canis familiaris	ENSCAFG00000019472	19 retrocopies	retro_cfam_1028, retro_cfam_1252, retro_cfam_1321, retro_cfam_1460, retro_cfam_1560, retro_cfam_1592, retro_cfam_1842, retro_cfam_1848, retro_cfam_1932, retro_cfam_1983, retro_cfam_2007, retro_cfam_2012, retro_cfam_2046, retro_cfam_2053, retro_cfam_2110, retro_cfam_271, retro_cfam_323, retro_cfam_490, retro_cfam_629,
Cavia porcellus	ENSCPOG00000011651	11 retrocopies	retro_cpor_1030, retro_cpor_1238, retro_cpor_1376, retro_cpor_1469, retro_cpor_1527, retro_cpor_177, retro_cpor_19, retro_cpor_437, retro_cpor_718, retro_cpor_769, retro_cpor_808,
Equus caballus	ENSECAG00000009065	7 retrocopies	retro_ecab_1025, retro_ecab_1105, retro_ecab_509, retro_ecab_632, retro_ecab_876, retro_ecab_892, retro_ecab_949,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Mus musculus	ENSMUSG00000044533	1 retrocopy	retro_mmus_148,
Pteropus vampyrus	ENSPVAG00000016704	8 retrocopies	retro_pvam_1395, retro_pvam_1486, retro_pvam_221, retro_pvam_240, retro_pvam_34 , retro_pvam_459, retro_pvam_521, retro_pvam_595,
Rattus norvegicus	ENSRNOG00000014179	12 retrocopies	retro_rnor_1882, retro_rnor_2191, retro_rnor_2257, retro_rnor_2274, retro_rnor_2903, retro_rnor_438, retro_rnor_631, retro_rnor_681, retro_rnor_690, retro_rnor_809, retro_rnor_810, retro_rnor_878,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,