RetrogeneDB ID: retro_pvam_459

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3251:49498..50361(-)
• Located in intron of: ENSPVAG00000009047

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_459
GGTACTGCAGGAAGCCCCGGAGGCCCAGGGGGCCCTGGGATGGGAGGCTGCAGCAGGTGGCATTGAGGATTTGGCAGTGG
CGTCCAGAGTAGAAGTCGTGGCCAAGGCCATAGCGAGGGTGAGGCCATGGCTATGGAGCTCGCAGAGGTAAGGCCAAGGA
CAAGGAATAGATCCCAGTCATCAAGCTGGGCCACCTGGTCAAGGACATAAAGATCAAGCCCCTGGAGGAGAATCTATCTC
TTCTCCCTGCCAATCAAGAAATCTGAGATCATTGACCTTTTCTTGGGGGCATCTCTCAAGGATGAGATTTTGAAAATTGT
GCGGTTGCAAAAGCAGACCCACAGTGGCCAGAAGACTCGGTTCAAGGCATTTGTCGCCATCGGGAACTACAATGGACATG
TCTGTTTGGGTGTTGAGTGTTCCAAGGAGGTAGCCACTGCCATCTATAGGGCCATCATCCTGGCTAAGCTCTCCATTGCC
CCTGTGAGGCGAGGCTGGGGGAACAAGATCTGCAGCCCCACATCATTCCTTGCAAGATGACTGGCCACTGTGGCTCTGTG
CCATGTGCCTCGTCCCTGTCCCCAGGGGCACTGGCATTGTCTCAGCCCCTGTGCCCAAGATGCTGTTGGTAAGCTGGTAT
CGTGGACGGCTACACCTCAGCCAGGGGCTGCACTGCCACCCTAGGCAACTTTGCCATGGCCACATTTGATGCCTTCTTTA
AGACCTATAGCTATCCCACCCCTGACCCCTGGAAGGAGACCGTGTTCGCCAAGTCTCCCTCGCAGGAATTCACTGACCAT
CTCGTAATGACCCACACCAGAATTTCTGTGCAGAGGACCCGGAATCCAGCTGTGGCCACCACA

Alignment

ORF - retro_pvam_459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.58 %
• Parental protein coverage: 98.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GAAGGPGGPGGPGIGGRGGFRGGFGSGI--RGRGRGRG-RGRGRGRGARGGKAEDKEWIPVTKLGRLVKD
          G.AG.PGGPGGPG.GG......GFGSG...R.RG.G...RG.G.G.GAR.GKA.DKE.IPV.KLG.LVKD
Retrocopy GTAGSPGGPGGPGMGGCSRWH*GFGSGVQSRSRGQGHS<RG*GHGYGARRGKAKDKE*IPVIKLGHLVKD

Parental  MKIKSLEE-IYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGV
          .KIK.LEE.IYLFSLPIK.SEIID.FLGASLKDE.LKI...QKQT..GQ.TRFKAFVAIG.YNGHV.LGV
Retrocopy IKIKPLEE>IYLFSLPIKKSEIIDLFLGASLKDEILKIVRLQKQTHSGQKTRFKAFVAIGNYNGHVCLGV

Parental  KCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIG-KPHTVPCKVTGRCGSV-LVRLIPAPRGTGIVSAPV
          .CSKEVATAI..AIILAKLSI.PVRRG.WGNKI...PH..PCK.TG.CGSV....L.P.PRGTGIVSAPV
Retrocopy ECSKEVATAIYRAIILAKLSIAPVRRG-WGNKIC<QPHIIPCKMTGHCGSV<AMCLVPVPRGTGIVSAPV

Parental  PKKLLMM-AGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHT
          PK..L...AGI.D.YTSARGCTATLGNFA.ATFDA..KTYSY.TPD.WKETVF.KSP.QEFTDHLV.THT
Retrocopy PK-MLLV>AGIVDGYTSARGCTATLGNFAMATFDAFFKTYSYPTPDPWKETVFAKSPSQEFTDHLVMTHT

Parental  RVSVQRTQAPAVATT
          R.SVQRT..PAVATT
Retrocopy RISVQRTRNPAVATT

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_459 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,