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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttatgttctctctaaaaagaatgcatttctgctcagtcactgtgctccttttatgctatctttcaagattgtacgtgacgtgcggttgttatttcaaatgttttagATTCCTTCATGGATCAATGAAAACAAAAGTGAGGGTCCTGTTAGCCATCCTTCTGATGTACAAATCCAACCAAATTCTGTTGGAAATGGTGTTGGTGTGA

Basic information

species Zea mays
transcript GRMZM2G024530_T01
intron # 4
splice site 3'
intron type U2

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|91055942|gb|EB166360.1|EB166360
EST:     GTAATCAAATTGCAGTTGCTGCAATGCCCGGATCACTGATCCCTCAAAAG                         ATTCCTTCATGGATCAATGAAAACAAAAGTGAGGGTCCTGTTAGCCATCCT
genomic: GTAATCAAATTGCAGTTGCTGCAATGCCCGGATCACTGATCCCTCAAAAGgtttttatgt ... aatgttttagATTCCTTCATGGATCAATGAAAACAAAAGTGAGGGTCCTGTTAGCCATCCT
EST: gi|18661470|gb|BM501414.1|BM501414
EST:     GTAATCAAATTGCAGTTGCTGCAATGCCCGGATCACTGATCCCTCAAAAG                         ATTCCTTCATGGATCAATGAAAACAAAAGTGAGGGTCCTGTTAGCCATCCT
genomic: GTAATCAAATTGCAGTTGCTGCAATGCCCGGATCACTGATCCCTCAAAAGgtttttatgt ... aatgttttagATTCCTTCATGGATCAATGAAAACAAAAGTGAGGGTCCTGTTAGCCATCCT
EST: gi|6536575|gb|AW224888.1|AW224888
EST:     GTAATCAAATTGCAGTTGCTGCAATGCCCGGATCACTGATCCCTCAAAAG                         ATTCCTTCATGGATCAATGAAAACAAAAGTGAGGGTCCTGTTAGCCATCCT
genomic: GTAATCAAATTGCAGTTGCTGCAATGCCCGGATCACTGATCCCTCAAAAGgtttttatgt ... aatgttttagATTCCTTCATGGATCAATGAAAACAAAAGTGAGGGTCCTGTTAGCCATCCT

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: 47 (upstream exon), 45 (downstream exon)
Score: 14

GAGCAAAATGCAGTGTGCAACGTTCCTATCCCTACGTTCACTGCACGTAATCAAATTGCAGTTGCTGCAATGCCCGGATCACTGATCCCTCAAAAGgtttttatgt ... aatgttttagATTCCTTCATGGATCAATGAAAACAAAAGTGAGGGTCCTGTTAGCCATCCTTCTGATGTACAAATCCAACCAAATTCTGTTGGAAATGGTGTTGGTGTGA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 37

GAGCAAAATGCAGTGTGCAACGTTCCTATCCCTACGTTCACTGCACGTAATCAAATTGCAGTTGCTGCAATGCCCGGATCACTGATCCCTCAAAAGgtttttatgt ... aatgttttagATTCCTTCATGGATCAATGAAAACAAAAGTGAGGGTCCTGTTAGCCATCCTTCTGATGTACAAATCCAACCAAATTCTGTTGGAAATGGTGTTGGTGTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

GAGCAAAATGCAGTGTGCAACGTTCCTATCCCTACGTTCACTGCACGTAATCAAATTGCAGTTGCTGCAATGCCCGGATCACTGATCCCTCAAAAGgtttttatgt ... aatgttttagATTCCTTCATGGATCAATGAAAACAAAAGTGAGGGTCCTGTTAGCCATCCTTCTGATGTACAAATCCAACCAAATTCTGTTGGAAATGGTGTTGGTGTGA


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 25

GAGCAAAATGCAGTGTGCAACGTTCCTATCCCTACGTTCACTGCACGTAATCAAATTGCAGTTGCTGCAATGCCCGGATCACTGATCCCTCAAAAGgtttttatgt ... aatgttttagATTCCTTCATGGATCAATGAAAACAAAAGTGAGGGTCCTGTTAGCCATCCTTCTGATGTACAAATCCAACCAAATTCTGTTGGAAATGGTGTTGGTGTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgctatctttcaagattgtacgtgacgtgcggttgttatttcaaatgttttagATTCCTTCATGGATCAATGAAAACAAAAGTGAGGGTCCTGTTAGCCATCCTTCTGATGTACAAATCCAACCAAATTCTGTTGGAAATGGTGTTGGTGTGA
                                     ttatttcaaatgtttt  TA-rich tract