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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatgtcttgagtgtattttccaattgcatattattttatttatgccacaccctaagtatctcttttatttgtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGACGGGAAGCTCCCACTGAATC

Basic information

species Zea mays
transcript GRMZM2G061745_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061745_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 6
gtta-atgtcttgag----tgtattttccaattgcatattattttatttatgccacaccctaagtatctcttttatttgtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGACGGGAAGCTCCCACTGAATC
|| | || ||   ||    || ||||||    | ||  ||  |||||| |||||  |   ||    |     || || |||| | ||||| || ||||||||||||||||| || ||||| || |||||||| |||||||||||  | || || |||||||||||||| |||||||||||||||||||
gtaatatttcacaagaatatgcattttcagcctacaagttgctttatt-atgccctaatatatcctttatcattgtt-gtcattaaagGTAACCAGCAAGCTTGCAGCCTTGAAAGGACTGGACGCAAGGCTCAGGGAGATCCGTGGGTACTTAGATCTTGTAATTGAAGGGAAGCTCCCACTGAATC
















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|60348273|gb|DN215246.1|DN215246
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
EST: gi|211385219|gb|FK956040.1|FK956040
EST:     CCTTCCYAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
genomic: CCTTCT-AAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
EST: gi|149014660|gb|EE044326.2|EE044326
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
EST: gi|148958380|gb|EC904610.2|EC904610
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATG
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATG
EST: gi|148960678|gb|EE011309.2|EE011309
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTNAAGGGACTCGATGCAAGGCTTAGGGAG
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
EST: gi|149013823|gb|EE043297.2|EE043297
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTANGGAG
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
EST: gi|50325946|gb|CO521072.1|CO521072
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
EST: gi|76015327|gb|DT942497.1|DT942497
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
EST: gi|149081616|gb|EE170759.2|EE170759
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
EST: gi|211382590|gb|FK956032.1|FK956032
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCYTAGGGAG
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
EST: gi|91055801|gb|EB166219.1|EB166219
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGA
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGA
EST: gi|211382594|gb|FK956036.1|FK956036
EST:     CCTTCMTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
genomic: CCTTC-TAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
EST: gi|78081122|gb|DV509534.1|DV509534
EST:     ACCTTCTAAGGGATGTCAGGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTAAAAGGGACTCGATGCAAGGCTTANGGAG
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
EST: gi|26456947|gb|CA828530.1|CA828530
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAA
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAA
EST: gi|148943844|gb|EC888923.2|EC888923
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTNAAGGGACTCGATGCAAGGCTT
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTT
EST: gi|148935087|gb|EC879128.2|EC879128
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
EST: gi|148971131|gb|EE021979.2|EE021979
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
EST: gi|62525906|gb|DN828554.1|DN828554
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTT
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTT
EST: gi|211385222|gb|FK956043.1|FK956043
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
EST: gi|149072304|gb|EE160567.2|EE160567
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATTGCA-GGCTTAGGGA
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGAT-GCAAGGCTTAGGGA
EST: gi|149107089|gb|EE188981.2|EE188981
EST:     ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG
genomic: ACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAG

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), 48 (downstream exon)
Score: 248

GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGACGGGAAGCTCCCACTGAATC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 221

GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGACGGGAAGCTCCCACTGAATC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 207

GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGACGGGAAGCTCCCACTGAATC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 238

GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAGgttaatgtct ... gtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGACGGGAAGCTCCCACTGAATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatattattttatttatgccacaccctaagtatctcttttatttgtcaattaagGTCACTAGCAAGCTTGCAGCCTTAAAGGGACTCGATGCAAGGCTTAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGACGGGAAGCTCCCACTGAATC
                                 tctcttttatttgtc  CT-rich tract
                                     ttttatttgtcaatta  TA-rich tract