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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGTTCAACTACATCAAAGAATCTTTTGAAAATGGTACTCTTCACCTTATTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaataatctttattcaatttatattagttaagttacaagcgtaccacaagatttacttttatttgctctatccag

Basic information

species Zea mays
transcript GRMZM2G003385_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003385_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g60190.2 (Oryza sativa), 5'ss of exon 3
TGGGTTCAACTACATCAAAGAATCTTTTGAAAATGGTACTCTTCACCTTATTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaa-taatctttatt--caatttatatta-gttaagttacaagcgtacca-caagatttacttttatttgctctatccag-----------
 |||||||| ||||||||||||| |||||| || ||||| || ||||||||||| |||||||||||||| || || |||||||| ||||| ||| |||||||||| |||    |  | | |  |   |||||||    |  |||       |||   |||  ||||  ||  | || ||| |               
GGGGTTCAATTACATCAAAGAATGTTTTGACAAGGGTACCCTGCACCTTATTGGTTTGTTGAGTGATGGAGGCGTTCACTCCCGTCTTGATCAAGTGCAGgtttgttaagctctgatgaatggcgccttatattgcaatgtgttgtttatttactgtcaatttttaaattggtgtgttctgtttcactctatttcag

upper sequence: GRMZM2G003385_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 5'ss of exon 3
TGGGTTCAACTACATCAAAGAATCTTTTGAAAATGGTACTCTTCACCTTATTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgt-----ttgctaataatctttattcaatttatattagtta-agttacaagcgtacca--------caagatttacttttatttgctctatc--cag
 || || || || ||||| || | |||||||| ||| ||  | ||||| |||||||||||||||||||| ||||||||||||||  |||| ||  |||| ||     ||| |  | |  | ||||   ||   ||| | || ||||       | |||        || |||   ||||   ||  ||| |   |||
AGGCTTTAAGTATATCAAGGAGTGTTTTGAAACTGGCACATTGCACCTCATTGGGTTGTTGAGTGATGGCGGTGTCCACTCCCGTATTGATCAGTTGCAAgtatgttttgttgttgaattctattaccttgtgattggatatagttttgtatttcccaggggagatcatgatcctctttggctttttctcttggcag

upper sequence: GRMZM2G003385_T02 (Zea mays), 5'ss of exon 4
lower sequence: EFJ26058 (Selaginella moellendorffii), 5'ss of exon 3
TGGGTTCAACTACATCAAAGAATCTTTTGAAAATGGTACTCTTCACCTTATTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaataatctttattcaatttatattagttaagttacaagcgtaccacaagatttacttttatttgctctatccag
 ||||||||  ||||||| ||  |||||   | |||||| || || || ||||| ||||||||||||||||||||||| ||  |    ||||| || |||||||  |     ||||| ||    || | |  ||   ||    |      | |  ||||| |                   
GGGGTTCAATCACATCAAGGAGGCTTTTCCTACTGGTACCCTCCATCTCATTGGATTGTTGAGTGATGGTGGTGTCCATTCTAGATACGACCAGCTTCAGgtttcttct---tctttctttcgcttttctgtgtggggtattga------ctctcgatttgcag-----------------

upper sequence: GRMZM2G003385_T02 (Zea mays), 5'ss of exon 4
lower sequence: EFJ14459 (Selaginella moellendorffii), 5'ss of exon 3
TGGGTTCAACTACATCAAAGAATCTTTTGAAAATGGTACTCTTCACCTTATTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaataatctttattcaatttatattagttaagttacaagcgtaccacaagatttacttttatttgctctatccag
 |||||||| |||||||| ||  |||||   | |||||| || || || ||||| ||||||||||||||||||||||| ||  |    ||||| || |||||||  |     ||||| ||    || | |  |    ||    |      | |  ||||| |                   
GGGGTTCAATTACATCAAGGAGGCTTTTCCTACTGGTACCCTCCATCTCATTGGATTGTTGAGTGATGGTGGTGTCCATTCTAGATACGACCAGCTTCAGgtttcttct---tctttctttcgcttttctgtgcggggtattga------ctctcgatttgcag-----------------

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|211278872|gb|FL399990.1|FL399990
EST:     TGGGTTGTTGAGNTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCNNNNNNNNTTCGTGTGCAC
genomic: TGGGTTGTTGAG-TGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCAC
EST: gi|211219836|gb|FL409202.1|FL409202
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCNNNNNNNNTTCGTGTGCAC
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCAC
EST: gi|211199735|gb|FL411304.1|FL411304
EST:     TGGGTTGTTGAGTGGATGGTGGTGTCCAGTCCCGCCTTGACCAACTACAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAGC
genomic: TGGGTTGTTGAGTG-ATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGC
EST: gi|211440955|gb|FL371600.1|FL371600
EST:     TTGGGTTGTYGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTACAG                         TTACTTCTGAAAGGTGTC
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTC
EST: gi|78085788|gb|DV514181.1|DV514181
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCNNNNNNNNTTCGTGTGCAC
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCAC
EST: gi|67022870|gb|CO451619.1|CO451619
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTACAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAGC
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGC
EST: gi|211027667|gb|FL415081.1|FL415081
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAG
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAG
EST: gi|76021242|gb|DT948412.1|DT948412
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCNNNNNNNNTTCGTGTGCAC
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCAC
EST: gi|211242233|gb|FL127853.1|FL127853
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCNNNNNNNNTTCGTGTGCAC
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCAC
EST: gi|211231748|gb|FL386170.1|FL386170
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCA-CTACAG                         TTACTTCTGAA-GGTGTCAGTGAGA
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGA
EST: gi|211397434|gb|FL369350.1|FL369350
EST:     TGGGTTGTTGAGNTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCNNNNNNNNTTCGTGTGCAC
genomic: TGGGTTGTTGAG-TGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCAC
EST: gi|211392275|gb|FL373437.1|FL373437
EST:     TGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGNAC-AACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCNNNNNNNNTTCGTGTGCAC
genomic: TGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTG-ACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCAC
EST: gi|211445807|gb|FL398454.1|FL398454
EST:     TGGGTTGTTGAGTGGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCNNNNNNNNTTCGTGTGCAC
genomic: TGGGTTGTTGAGTG-ATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCAC
EST: gi|211106346|gb|FL370787.1|FL370787
EST:     TGGGTTGTTGAGTGGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCNNNNNNN-TTCGTGTGCAC
genomic: TGGGTTGTTGAGTG-ATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCAC
EST: gi|211005730|gb|FL388917.1|FL388917
EST:     TGGGTTGTTGAGTGNATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCNNNNNNNNTTCGTGTGCAC
genomic: TGGGTTGTTGAGTG-ATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCAC
EST: gi|31611945|gb|CD568567.1|CD568567
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCNNNNNNNNTTCGTGTGCAC
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCAC
EST: gi|211527387|gb|FL402925.1|FL402925
EST:     TGGGTTGTTGAGTTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCNNNNNNNNTTCGTGTGCAC
genomic: TGGGTTGTTGAGT-GATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCAC

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: 443

TGGGTTCAACTACATCAAAGAATCTTTTGAAAATGGTACTCTTCACCTTATTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCACATCCTTACCGATGGGCGTGACGTTTTGGATGGCAGCAGTGTTGGTTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 799

TGGGTTCAACTACATCAAAGAATCTTTTGAAAATGGTACTCTTCACCTTATTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCACATCCTTACCGATGGGCGTGACGTTTTGGATGGCAGCAGTGTTGGTTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 766

TGGGTTCAACTACATCAAAGAATCTTTTGAAAATGGTACTCTTCACCTTATTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCACATCCTTACCGATGGGCGTGACGTTTTGGATGGCAGCAGTGTTGGTTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 793

TGGGTTCAACTACATCAAAGAATCTTTTGAAAATGGTACTCTTCACCTTATTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGAGCAAAAAAAATTCGTGTGCACATCCTTACCGATGGGCGTGACGTTTTGGATGGCAGCAGTGTTGGTTTCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGTTCAACTACATCAAAGAATCTTTTGAAAATGGTACTCTTCACCTTATTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGCCTTGACCAACTGCAGgtttgctaataatctttattcaatttatattagttaagttacaagcgtaccacaagatttacttttatttgctctatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG