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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgcctgctccttacccatttccccccctccctcgcggaatttgaggatttgtgaggcccgcggaggcttcgctcgattggtttcctggcggctaattggtttgatttggttgcttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG

Basic information

species Zea mays
transcript GRMZM2G008259_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008259_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g14010.1 (Oryza sativa), 3'ss of exon 1
----------------------------gtacgcgcctgctccttacccatttccccccctccctcgcggaatttgaggatttgtgaggcccgcggaggct----tcgctcgattggtttcctg---------------gcggctaat--tggtttgatttggttgcttcct--------tgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
                            ||  | ||   | |        |||  |    ||  |   | ||    |   |  ||| |    |  | ||      | | ||| |||| || |||               | |||| ||  ||||||| || | ||  ||  |        |||||| ||||||||||||||||||||||| |||||||
gtatggaggggggaagaggggtctctcggtttgagctctcacgcggatgctttttctttttcttttttgaaaggaaaaattgggtgggttttgaaggggtactgattgatcggttgggttgctgatgagtggtgaatgagtggctgattttggtttggttggatttttttttgtttcttttgcagATGTGGAGAAGTTCTACCAGCAGTGCGACCCAG
















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|60341456|gb|DN208429.1|DN208429
EST:     CGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|101398089|gb|EB820919.1|EB820919
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|149070148|gb|EE158549.2|EE158549
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|76916780|gb|DV166549.1|DV166549
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|76290977|gb|DV030545.1|DV030545
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|76281879|gb|DV021447.1|DV021447
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|22819609|gb|BU499699.1|BU499699
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|28910319|gb|CB331379.1|CB331379
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|148930178|gb|EC872565.2|EC872565
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|22819406|gb|BU499496.1|BU499496
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|78114017|gb|DV532406.1|DV532406
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|9794347|gb|BE552655.1|BE552655
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|149075823|gb|EE164362.2|EE164362
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|78118666|gb|DV537050.1|DV537050
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|149106607|gb|EE188500.2|EE188500
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|149008353|gb|EE040506.2|EE040506
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|50338834|gb|CO533960.1|CO533960
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|74236627|gb|DT644541.1|DT644541
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|26559804|gb|CA832039.1|CA832039
EST:     GGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: GGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|71766893|gb|DR964830.1|DR964830
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|13490681|gb|BG517445.1|BG517445
EST:     CGGGATTTCCGCGCGCGGCGGGCTGGTATGTATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CGGGATTTCCGCGCGCGGCGGGCTGGTATG-ATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
EST: gi|78120146|gb|DV538530.1|DV538530
EST:     CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCG                         ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
genomic: CCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG

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: 526

CACTGGGAGATGGACGGCGGCGGCACGCACCGCACGCCGGAAGACGTGTTCCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 105

CACTGGGAGATGGACGGCGGCGGCACGCACCGCACGCCGGAAGACGTGTTCCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 94

CACTGGGAGATGGACGGCGGCGGCACGCACCGCACGCCGGAAGACGTGTTCCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 75

CACTGGGAGATGGACGGCGGCGGCACGCACCGCACGCCGGAAGACGTGTTCCGGGATTTCCGCGCGCGGCGGGCTGGTATGATCAAAGCGCTCACCACCGgtacgcgcct ... ttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgctcgattggtttcctggcggctaattggtttgatttggttgcttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG
                                         ttgcttcctt  CT-rich tract
                               tttgattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcgcctgctccttacccatttccccccctccctcgcggaatttgaggatttgtgaggcccgcggaggcttcgctcgattggtttcctggcggctaattggtttgatttggttgcttccttgcagACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT