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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaatagccagacagtcgtgcaattcctatcgctaccgcttttaatttaataacatgtgttaatttattgagcag

Basic information

species Zea mays
transcript GRMZM2G062042_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 26
AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaatagccagacagtcgtgcaattcctatcgctaccgcttttaattt-aataacatgtgtt---aatttattgagcag
| | |||||||| |||||||| ||||| ||||| || ||||||||||||||||| ||||| ||||||||||||||||| ||||| |||||||||||||||||||| | | | || | | | || || | | || ||||| ||| |||||| || ||| |||| |||
ATCTTTGAATGAGCTTTATGTTGAAGAGGAGGATTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAGAAGgtaaagcgattagatgattgtactgct-tattgatgttatttttccttttttttttattttgaataactaatggctggaatgccttgatcag

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 26
AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaatag--ccagacagtcgtgcaattcctatcgctaccgcttttaatttaataacatgtgtt---aatttattgagcag
||| |||||||| |||||||| ||||| |||||||| ||||||||||||||||| ||||| ||||||||||||||||| ||||| ||||||||||| |||||||| | ||| || | | | | || ||| | | | ||| || |||||| || ||| |||| |||
AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgattatatgattgtactgcttattgatgttattttt-ccttttttattttattttgaataactaatggctggaatgccttgatcag

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 26
AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaat-------agccagacagtc-gtgcaattcctatcgctaccgcttttaatttaataacatgtgttaatt--tattgagcag----------------------
|| ||||||||| |||||| || || || ||||| || ||||||||||||||| | || ||||||| ||||| || ||||| |||||||| |||||||| || | || | | |||| | | || || | | | | ||| || | | |||| |||||| |
GGCTTTGAATGAAATTTATGCTGAGGAAGAAGACTATGACAGACTCCGTGAATCAATAGATCTGCATGATAACTTCGATCAGATAGGTCTTGCACAGAAGgtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcag

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 24
AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaa------ataaaaataaaatagccaga-cagtcgtgcaattcctatcg------ctaccgct--tttaatttaataacatgtgttaatttattgagcag
||| ||||||||| ||||||| || || |||||||| || ||||| | ||||||| | || ||||||||||||| || ||||| |||||||| |||||||| || || | |||| || | | | | | || || | || | | ||| ||| | | |||| || ||| ||
AGCTTTGAATGAAATTTATGTTGAGGAGGAGGACTATGATAGACTTCATGAATCAATAGATCTGCATGACAACTTCGATCAGATAGGTCTTGCACAGAAGgtgaatcttccgtatctttcaaattgctaaaattgaaatctgaatcttactgagaaacttaggggtcatttggtttgaagaaatgtttttttttttttct---

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 26
AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaa------taaaaataaaatagccaga-cagtcgtgcaattcctatcgctaccgctt--ttaatttaataacatgtgttaatttattgagcag----
||| ||||||||| ||||||| || || |||||||| || ||||| | ||||||| | || ||||||||||||| || ||||| |||||||| |||||||| || || | |||| || | | | | | || || || || | | ||| | | || |||| ||
AGCTTTGAATGAAATTTATGTTGAGGAGGAGGACTATGATAGACTTCATGAATCAATAGATCTGCATGACAACTTCGATCAGATAGGTCTTGCACAGAAGgtgaatcttccttatctttcaaattgctaaaattgaaatctgaatcttaccgagacatttgggtgtgtttggtt-tgcattttcattttctgttttcattt

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 26
AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaat-------agccagacagtcgtgcaattcctatcgctaccgcttttaatttaat-aacatgtgttaatt--tattgagcag--------------------
||| ||||||||| ||||||| || || || |||||||| |||||||| |||||| | || |||||||||||||||| ||||| |||||||| |||||||| || || | | |||| | || || | | || | | | || |||| | |||| |||||| |
AGCTTTGAATGAAATTTATGTTGAGGAAGAAGACTACGACAGACTCCGAGAATCAATAGATTTGCATGACAACTTTGATCAGATAGGTCTTGCACAGAAGgtgaatctcggttatcttttgtcttattttgacaattagcaaaatctgagatcaggaagttatggaaaatttaaaatgtttgaattattattgattggcttcaacaatacatgagcag

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 26
AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaatagccagacagtcgtgcaattcct----------atcgctaccgcttttaatttaataacatgtgttaatttattgagcag----
|| ||||||| | || || ||||| || |||||||| || | || || || |||| | ||||||| ||||||||||||||| || || ||||||||||| | ||||| | || || | | | || | | | || || | | ||| || | | || | ||
GGCTCTGAATGAGATATACGTGGAAGAAGAAGACTACGATAGGTTGCGAGAGTCTATTGATTTACATGACAGCTTTGACCAGATTGGCCTCGCTCAGAAGgtaaagttcaaatatactacccctttaatattttctctctttaaaaatggaaaaagaatggccttagagatgatataatcttcctgtgaatggtgcgaacag

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 26
AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaatagccagacagtcgtg-caattcctatcgctaccgcttttaatttaataacatgtgttaatttat-tgagcag
||| || |||| || |||| || || |||||||| || ||||| || |||||| | || |||||||| |||||||||||||| || ||||| |||||||| | | | | || || | | | || | || | | | || |||| || | | || | || |||
AGCATTAAATGGTATTCATGTAGAGGAGGAGGACTATGATAGACTTCGGGAATCAATAGATATGCATGATAACTTTGACCAGATAGGCCTTGCACAGAAGgtgagagagattgaatttattttgttaatgttggtaggcttcataagcagaacatgtac----ataagatctagtgatgcgtgtggacag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|26455954|gb|CA827537.1|CA827537
EST:     AATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG                         CTTGAGAAGCATGAAATGCTGGAGATGAGGAGGATCGCCGCCTACATTTAC
genomic: AATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaa ... tattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTAC
EST: gi|19770178|gb|BQ034899.1|BQ034899
EST:     AATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG                         C-TGAGAAGCATGAAATGCTGGAGATGAGGAGGATCGCCGCCTACATTTAC
genomic: AATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaa ... tattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTAC
EST: gi|211415581|gb|FL028985.1|FL028985
EST:     CATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG                         CTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTAC
genomic: CATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaa ... tattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 451

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaa ... tattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCCATTGCTCTATCGAAGAAAGACA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 284

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaa ... tattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCCATTGCTCTATCGAAGAAAGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaa ... tattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCCATTGCTCTATCGAAGAAAGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaa ... tattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCCATTGCTCTATCGAAGAAAGACA