RetrogeneDB ID:

retro_pvam_221

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:GeneScaffold_1976:311568..312377(-)
Located in intron of:ENSPVAG00000017426
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS2
Ensembl ID:ENSPVAG00000016704
Aliases:None
Description:ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]


Retrocopy-Parental alignment summary:






>retro_pvam_221
GGTGCTACGGGAGGGTCTGGAGGCCCCAGAGGCCCTGGAATGGGAGGCCACTGCAGCTTCCTTGGAGGATTCCGTAACAG
TGTCTAGGGTGGAGGTCAAGGCCAGGGTCGCAAGAGGTGGATCCCTGTCACCAAGCTGGGCCGCCTGGTCAAGAATATGA
AGATCAAGTCCCTGGAGATCTAACTCTTCTCCTTGACCATCAAGGAATCTGAGATCAATGACTTTTTCATGCATACATCC
TTCAAGGATGAGGTTTTAAAGATTATGCTGGTGCAAAAGCAGACCCACGCTGGAGAGGACCCAGTTCAAGGTATCTGTTG
CATCAAGGACTATAATGGTCATGCCGGTTTGGGTGTTAAGTGCTCCAAGGAGGTTGCCACTGCCATCCACATGGGGCTAT
TATCCCCGACAAGCTCTCCACCTCTGTGCGGCAAGGCTACTGAGAGAACAAAATCGGCAAACCCCACACCATCCCTTGCA
AGGTGACCAGCTGCTGTGGCTCTGTGTTTGTGTGCCCTACCCACATCCCCAGGGGCATTGGCATTGTCTCAGCCCATGTC
CAAGAAGCTGCTGATGATGGCTGGTATTGATGACTGCTACACCTCAGCCAGGGGCTGCACTGCCACTCTGGGCAACTTCA
CCAAGGCCACCTGTGATGCCATCTCTAAGACCTACAGTTATTTCACTCCCAACCACTGGAAAGAATTGTCATTCACCAAA
TGTTCCTATCAGGAATTCACTGACCATGTTGCAAAGCTCCACAGAGAGGTTCTGTGCAGAGGACCCAGGCTCCAGCTGTG
GCCACCACA

ORF - retro_pvam_221 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.83 %
Parental protein coverage: 93.52 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalGGRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEWIPVTKLGRLVKDMKIKSLEEIYLFSLPIK
G..GG..G..G.G..G.....G..R....G...G....K.WIPVTKLGRLVK.MKIKSLE.I.LFSL.IK
RetrocopyGATGGSGGPRGPGMGGHCSFLGGFRNSV*GGGQGQGR-KRWIPVTKLGRLVKNMKIKSLE-I*LFSLTIK
ParentalESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAI-ILA
ESEI.DFF...S.KDEVLKIM.VQKQT.AG..........I.DYNGH.GLGVKCSKEVATAI.....I..
RetrocopyESEINDFFMHTSFKDEVLKIMLVQKQTHAGE-DPVQGICCIKDYNGHAGLGVKCSKEVATAIHMGL<IIP
ParentalKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSA-PVP-KKLLMMAGIDDCYTSA
......VR.GY..NKIGKPHT.PCKVT..CGSV.V.....PRG.GIVSA.P.P.KKLLMMAGIDDCYTSA
RetrocopyDKLSTSVRQGY*ENKIGKPHTIPCKVTSCCGSVFVCPTHIPRGIGIVSA<PCP<KKLLMMAGIDDCYTSA
ParentalRGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRV-SVQRTQAPAVATT
RGCTATLGNF.KAT.DAISKTYSY.TP..WKE..FTK..YQEFTDH..K.H..V.SVQRTQAPAVATT
RetrocopyRGCTATLGNFTKATCDAISKTYSYFTPNHWKELSFTKCSYQEFTDHVAKLHREV<SVQRTQAPAVATT

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Pteropus vampyrus was not studied using RNA-Seq expression data.
Pteropus vampyrus was not studied using ChIP-Seq data.
Pteropus vampyrus was not studied using EST data.
Pteropus vampyrus was not studied using FANTOM5 data.
retro_pvam_221 was not experimentally validated.

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 9 parental genes, and 65 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000025491 retrocopy
Canis familiaris ENSCAFG0000001947219 retrocopies
Cavia porcellus ENSCPOG0000001165111 retrocopies
Equus caballus ENSECAG000000090657 retrocopies
Monodelphis domestica ENSMODG000000160771 retrocopy
Mus musculus ENSMUSG000000445331 retrocopy
Pteropus vampyrus ENSPVAG00000016704 8 retrocopies
Rattus norvegicus ENSRNOG0000001417912 retrocopies
Sarcophilus harrisii ENSSHAG000000152135 retrocopies



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