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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgttatggatagcaaatattctactgcgtcattactgtgctcttgttgaatctgaaccattgtttttctag

Basic information

species Zea mays
transcript GRMZM2G108829_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 5'ss of exon 2
TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgta----aatatgttatggatagcaaatattctactgcgtcattactgtgctcttgttgaatctgaaccattgtttttctag
|||||||||||||||||||| |||||||| ||||||||||| ||||||||  | |||||||| ||||||||||||||||||||||||||||||    |  |||| ||  |  |||||  ||  | |   ||  ||  |  || ||||| | |||   ||  |||| ||| ||
TCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATAAGGGAAAATGACATATTATACTTCATAATGGAATACATGgtacttaaggatgtcatataccgcaaaagtttaattagctctgtatcg--cttttgttaagtct---cccatgttcttccag

upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA09G34610.1 (Glycine max), 5'ss of exon 4
TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaat-----atgttatggatagcaaatattctactgcgtcattactgtgctc---ttgttgaatctga-accattgtttttctag-----
|| || ||    |||||||| || || ||||||||||| ||||| ||||| ||||||| |||||| || |||||  |  | || ||||||||   |     |  || | | |||  ||        |  ||   | |          ||  | | | | |   || | |||   |       
TCATTACGAAAAATGAATCACCCAAATATTGTGAAGCTGAAAGAAGTTATTCGAGAAAGTGATATCTTGTACTTTGTTTTTGAGTACATGgtgggtgactaaacttcttggtagagaaaggctaggttggtggatgcaagatctaatttactaattttaatgtcaatttttgggtgatgtag

upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT4G19110.1 (Arabidopsis thaliana), 5'ss of exon 6
TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgtta-----tggatagcaaatattctactgcgtcattactg--tgctcttg-ttgaatctgaaccattgtttttctag---
||  |  || | ||||||||||| |||||||||||| | || || || ||||| |||||||||||  |||||||  |  | || ||||||||| |  | ||      | | |   |  |||| |         ||| |   ||||||   |  | | |    |||| ||| |  |    
TCGCTCAGGAGAATGAATCATCCAAACATTGTGAAGTTGAAGGAAGTAATCCGGGAAAATGATATCCTATACTTTGTCTTTGAGTACATGgtatacttctttcctgcttgttgttaggtattttctgatacttttattcattgctctgaatctactttatgtcattctttcttgatcag

upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT5G45430.1 (Arabidopsis thaliana), 5'ss of exon 6
TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgttatggatagcaaat--attctactgcgtcattactgtgctcttgttgaatctgaaccattgtttttctag-----
||  |  |  | ||||||||||| |||||||||||||| || || || ||||| |||||||||||  |||||||  |  | || ||||||||| |  | ||     |      |  ||  || |||  ||  ||| |  | |   | |||||    |  | |  | ||       
TCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATGgtatacttctttctactttttgcttaatcttattgc--caacacttttttttctctaaatcttcttccctttcatactctgtcag

upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S173_136V6.1 (Physcomitrella patens), 5'ss of exon 4
TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatat---gttatggatagc---aaatattctactgcg-----tcattactgtgctcttgttgaatctgaaccattgtttttctag---------------------------------------
|||||||||    |||||||||||||||| |||||||| || ||||||||||| ||||| |||  | | |  ||| |  | || || ||||| |   |   | | |  |  ||   | | ||  ||| ||      |   |  | || |  |  ||    | ||  || |   ||   |                                       
TCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATCCGTGAAAACGATGAACTGTTTTTCGTTTTTGAGTATATGgtgaggttttagcttttcacggctctagaaatggtacagcaattatttgatggtttgtttcttctgggattaaatgatggacattggtgtaatattcctttcaatattgtttgcatttaatcgtgcag

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|211496286|gb|FL041698.1|FL041698
EST:     AAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG                         GAGTGTAATCTCTACCAACTTATGAAGGATAAGGTCAAGCCTTTCTCGGAG
genomic: AAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttctagGAGTGTAATCTCTACCAACTTATGAAGGATAAGGTCAAGCCTTTCTCGGAG
EST: gi|31350422|gb|CD434779.1|CD434779
EST:     AAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG                         GAGTGTAATCTCTACCAACTTATGAAGGATAAGGTCAAGCCTTTCTCGGAG
genomic: AAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttctagGAGTGTAATCTCTACCAACTTATGAAGGATAAGGTCAAGCCTTTCTCGGAG
EST: gi|47961778|gb|CN844487.1|CN844487
EST:     AAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG                         GAGTGTAATCTCTACCAACTTATGAAGGATAAGGTCAAGCCTTTCTCGGAG
genomic: AAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttctagGAGTGTAATCTCTACCAACTTATGAAGGATAAGGTCAAGCCTTTCTCGGAG
EST: gi|67011156|gb|CO439905.1|CO439905
EST:     AAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG                         GAGTGTAATCTCTACCAACTTATGAAGGATAAGGTCAAGCCTTTCTCGGAG
genomic: AAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttctagGAGTGTAATCTCTACCAACTTATGAAGGATAAGGTCAAGCCTTTCTCGGAG
EST: gi|211496285|gb|FL041697.1|FL041697
EST:     AAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG                         GAGTGTAATCTCTACCAACTTATGAAGGATAAGGTCAAGCCTTTCTCGGAG
genomic: AAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttctagGAGTGTAATCTCTACCAACTTATGAAGGATAAGGTCAAGCCTTTCTCGGAG

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: 191

TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttctagGAGTGTAATCTCTACCAACTTATGAAGGATAAGGTCAAGCCTTTCTCGGAGTCTGAAGTCCGCAACTGGTGCTTTCAGATATTTCAGGCTCTTGCTTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttctagGAGTGTAATCTCTACCAACTTATGAAGGATAAGGTCAAGCCTTTCTCGGAGTCTGAAGTCCGCAACTGGTGCTTTCAGATATTTCAGGCTCTTGCTTACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 95

TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttctagGAGTGTAATCTCTACCAACTTATGAAGGATAAGGTCAAGCCTTTCTCGGAGTCTGAAGTCCGCAACTGGTGCTTTCAGATATTTCAGGCTCTTGCTTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 234

TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttctagGAGTGTAATCTCTACCAACTTATGAAGGATAAGGTCAAGCCTTTCTCGGAGTCTGAAGTCCGCAACTGGTGCTTTCAGATATTTCAGGCTCTTGCTTACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgttatggatagcaaatattctactgcgtcattactgtgctcttgttgaatctgaaccattgtttttctag

- - - - - - - - - - - - - - - - - - - - AAGAGG