RetrogeneDB ID:

retro_ttru_1002

Retrocopy
location
Organism:Dolphin (Tursiops truncatus)
Coordinates:GeneScaffold_957:108229..108626(+)
Located in intron of:ENSTTRG00000012133
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CHMP1B
Ensembl ID:ENSTTRG00000008066
Aliases:None
Description:charged multivesicular body protein 1B [Source:HGNC Symbol;Acc:24287]


Retrocopy-Parental alignment summary:






>retro_ttru_1002
TTTAACTTGTAGTTTGCTGTCAGAGAACTTAATAACAATGCCAAGAAATATGAGAGAGAAGAAAAGGCTGGAAAGGTCAA
GATTAAAAAGGCCATTTAGAAGAGCAGTCCAGAAGAGGCAAGAATACACATTGAAAATGCAATCCACCAGAGGAAACAAG
CAATTAATTTCTGGAGTGTGAGTGCTGGGGCTCCTGCTGTGGCAGCAGGAGTTCAGACTACGGGCAAGGTGACAAAGTTC
ACAGCCGTTGGTTGGCTCTGCAGATGCTACATGGAGGGGTATGAACCTCCATGAAAAGATGTTTGTCCCGATGGACACGT
GTAAACACCAACTGGAAATGCTGAAGGTTCAAACGCAACAAAGGGAAGACACGATGAGTCACTCCACAACCCTAACA

ORF - retro_ttru_1002 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.96 %
Parental protein coverage: 68.34 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalFNLKFAAKELNRNAKKCDKEEKAEKAKIKSLKQAIQKGNTEAAR-HAENAIRQKNQTINFLRMSARVDAV
FNL.FA..ELN.NAKK...EEKA.K.KI...K.AI.K...E.AR.H.ENAI.Q..Q.INF...SA...AV
RetrocopyFNL*FAVRELNNNAKKYEREEKAGKVKI---KKAI*KSSPEEARIHIENAIHQRKQAINFWSVSAGAPAV
ParentalAARVQTAVTMGKVS-SQRYVVKSMDATLRSRTL-KRISALMDKFEQQFETLDVQTQQMEDTMSSTTTLT
AA.VQ...T.GKV..S....V.S.DAT.R...L.......MD....Q.E.L.VQTQQ.EDTMS..TTLT
RetrocopyAAGVQ---TTGKVT>SSQPLVGSADATWRGMNLHEKMFVPMDTCKHQLEMLKVQTQQREDTMSHSTTLT

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






Tursiops truncatus was not studied using RNA-Seq expression data.
Tursiops truncatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ttru_1002 retrocopy.
Tursiops truncatus was not studied using FANTOM5 data.
retro_ttru_1002 was not experimentally validated.

Retrocopy orthology:
Tursiops truncatus 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 16 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000266601 retrocopy
Equus caballus ENSECAG000000186251 retrocopy
Gorilla gorilla ENSGGOG000000256041 retrocopy
Loxodonta africana ENSLAFG000000264572 retrocopies
Macropus eugenii ENSMEUG000000152502 retrocopies
Myotis lucifugus ENSMLUG000000248113 retrocopies
Monodelphis domestica ENSMODG000000042732 retrocopies
Mus musculus ENSMUSG000000312421 retrocopy
Ochotona princeps ENSOPRG000000185561 retrocopy
Pongo abelii ENSPPYG000000205051 retrocopy
Pteropus vampyrus ENSPVAG000000014162 retrocopies
Rattus norvegicus ENSRNOG000000023232 retrocopies
Sarcophilus harrisii ENSSHAG000000169032 retrocopies
Tarsius syrichta ENSTSYG000000117271 retrocopy
Tursiops truncatus ENSTTRG00000008066 2 retrocopies
retro_ttru_1002 , retro_ttru_235,
Vicugna pacos ENSVPAG000000008542 retrocopies



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