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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAGGTGTTACTGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgactctcttcttcctgttgcatctgaaaaaatggtgagatgtcttatatcatatcaacagtcttgtaaaaaattgttgcacttagtgcttgtt...

Basic information

species Zea mays
transcript GRMZM2G107639_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107639_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g08270.1 (Oryza sativa), 5'ss of exon 6
GCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAGGTGTTACTGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgactctcttcttcctgttgc-atctgaaaaaatggtgagatgtcttatatcatatcaacagtcttgtaaaaaattgttgc-acttagtgcttgtt---
||||| ||||| |||||| ||||||||||||||||||||||||| ||||||||||||||||||||||   || ||||  |||| |||||||||||||| ||||||||   |||   |||  | ||    |  || ||| |||| |||||||| ||    |||||||||||   || ||| | ||||| ||||  |    | |   
GCACCATATTACTTCAATTCCTACATGTCATTCCAGATGACAGGAGTTACTGACATATTAGTTGGTGCAAGCAATCCTGAGACTCTTCATCCTGATGTCGgtaagatagttcttccctttttctttttgttggagaaattggttagatgtct-at----tatcaacagtcaattataaactagttgccactttttttccgcttct

upper sequence: GRMZM2G107639_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G43830.2 (Glycine max), 5'ss of exon 5
GCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAGGTGTTACTGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgactc-tcttcttcctgttgcatctgaaaaaatggtgagatgtcttatatca-tatcaacagtcttgtaaaaaattgttgcacttagtgcttgtt
|| || || || ||||||||||||||||| ||||||||||| || |||||  | ||  ||||||||    |     |  | ||||| ||||||||||  ||||| | |   | |  |||   |  || |    |     |  ||  |||   || |  |  |    || |||| |      |    |||  |  |       
GCTCCTTACTACTTCAATGCCTACATGTCCTTCCAGATGACTGGCGTTACCAATATTCTAGTTGGTCCTGGTAGCTCAGACACACTCCATCCTGATGCAGgtaaaaagttgcatgatctggttactgtaatccattttttactggcatggactagagaagcaaaggcaatctt-tggttgctaagagcatcttttttcctc-

upper sequence: GRMZM2G107639_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv09s0002g05250.t01 (Vitis vinifera), 5'ss of exon 5
GCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAGGTGTTACTGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgactctcttcttcct-gttgcatctgaaaaaatggtgagatgtcttatatcatatcaacagtcttgtaaaaaattgttgcacttag--tgcttgtt
||||| || || |||||||| |||||||| ||||||||||||||||||||| ||||||| || |||   |   |||| ||||| |||||||| ||||  ||||||  |  ||| |   || |  ||| || | |||| ||  |  ||||   | | ||  | |  ||   |||   |   |   |   ||||   ||  ||| 
GCACCATACTACTTCAATGCATACATGTCCTTCCAGATGACAGGTGTTACTAACATATTGGTGGGTCCTTCTAATCCGAAGACTCTTCATCCAGATGCAGgtaaggagtttctttaactcttcattgtatat-aaaacatattctgatgatat-tttctgaacttcaactttgatgatcctgccttttcttaaattggatgt-

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|148932368|gb|EC876010.2|EC876010
EST:     TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTG                         ATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
genomic: TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
EST: gi|67030337|gb|CO459086.1|CO459086
EST:     TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTG                         ATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
genomic: TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
EST: gi|211010784|gb|FL361163.1|FL361163
EST:     TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTG                         ATTGGGTTGGAGAAG-TTCNNTGAA-GAAA-TGAGCCTATCCCTAAACTTG
genomic: TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGG-TTGGAGAAGGTTC--TGAAAGAAAATGAGCCTATCCCTAAACTTG
EST: gi|148947797|gb|EC893285.2|EC893285
EST:     TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTG                         ATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
genomic: TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
EST: gi|148963140|gb|EE014107.2|EE014107
EST:     TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTG                         ATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
genomic: TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
EST: gi|149112179|gb|EE295100.2|EE295100
EST:     TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTG                         ATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
genomic: TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
EST: gi|149037081|gb|EE155270.2|EE155270
EST:     TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTG                         ATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
genomic: TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
EST: gi|149084340|gb|EE173781.2|EE173781
EST:     TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTG                         ATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
genomic: TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
EST: gi|76286951|gb|DV026519.1|DV026519
EST:     TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTG                         ATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
genomic: TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
EST: gi|50325408|gb|CO520534.1|CO520534
EST:     TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTG                         ATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
genomic: TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
EST: gi|148990980|gb|EE032414.2|EE032414
EST:     TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCCTCCTGATGTTG                         ATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
genomic: TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
EST: gi|149014921|gb|EE044649.2|EE044649
EST:     TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTG                         ATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
genomic: TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
EST: gi|67011573|gb|CO440322.1|CO440322
EST:     TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTG                         ATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
genomic: TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCA
EST: gi|148931036|gb|EC873618.2|EC873618
EST:     TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTG                         ATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCT
genomic: TGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCT

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: 152

GCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAGGTGTTACTGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCACTGTTGTGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 380

GCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAGGTGTTACTGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCACTGTTGTGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 296

GCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAGGTGTTACTGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCACTGTTGTGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 821

GCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAGGTGTTACTGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgac ... aaaaatgcagATTGGTTGGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCACTGTTGTGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAGGTGTTACTGACATATTAGTTGGTGGCTGCGATCCCAAGACACTTCATCCTGATGTTGgtaagatgactctcttcttcctgttgcatctgaaaaaatggtgagatgtcttatatcatatcaacagtcttgtaaaaaattgttgcacttagtgcttgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaaaa