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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatctgcaaggctctagttttatgttcccttcatctttttaaaattctttctctatcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG

Basic information

species Zea mays
transcript GRMZM2G458208_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 5
-------------------gtatatct-gcaaggctctagttttatgttcc---cttcatct-ttttaaaattctttctctatcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG
                   | | ||||    | |   | |  || | |      ||| |||| ||   || |||||    |    | | |||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||| ||||| ||||||
gtaatacttgtgattcattgcagatctcattatgtgtttgacttgtttcttaatcttaatctgttactaagttcttatgttcatatataaagGTGGGCACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCG

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 5
-----------------------------gtatatctgcaaggctctagttttatgttcccttcatctt--tttaaaattctttctctatcctg---tga-agGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG
                              | ||| |   |||   |  |  || |  | ||   | ||   ||||  |   || |  |   ||   ||| |||| || |||||||| || || || || || |||||||||||| | ||||| || ||||||||||| |||||||||||||| || ||||| ||| | 
gtttgtcaatcaaactttgctagagcctcttgtatattgcaggagatgataataaggactctgagttttaacttaatttatgtttttgaatttgaattgatagGTAGGGACAATATCTGCTAACGGAGAGAGAGAAATTGGTGAGTTGATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------gtatatctgcaaggctctagttttatgttcccttcatctttttaaaattctttctctatcctgtga-agGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG
                                                        | | |   |||| | | |   | ||      |   |     |      ||| |  ||   |||| |||| || |||||||| || |||||||| ||||||||||||||| | ||||| || ||||||||||| ||||||||||||||||||||||| ||  | 
gtttgtgtatctttcttttttattggagccactacttgcattgtgggagattgaaaacaacaagaaggattttgaactgtgagagtattgacaaaacattgcaatttataaatatggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACAATCTCA

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 5
----------------------------------------------gtatatctgcaagg-ctctagttttatgttcccttcatctttttaaaattctttctctatcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG
                                                ||      ||||  ||| | |||    |    |     ||||  |||| |   | |    ||   |||| || |  ||||| || ||||| || || |||||||||||| | ||||| || ||||||||||| |||||||||||||| || ||||| ||| | 
gtttgtcgatcatactttgctagagcctcttcttgtatattgcaggagatgataataaggattctgggttttaactttaatttctgtttttgaattttgaatttgaattg-atagGTTGGGATGATATCTGCTAATGGAGAGAGAGAAATTGGTGAGTTGATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------gtatatctgcaaggctctagttttatgttc--ccttcatctttttaaaattc---tttctctatcctgtga-agGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG
                                               | | || || ||    | ||  | || ||   || |  | ||   |||  |    ||  |  ||   |||| |||| || |||||||| || |||||||| ||||||||||||||| | ||||| || ||||||||||| ||||||||||||||||||||||| ||  | 
gtttgtgaatcttccttttttgttggagccactactggcatattgcaggagat-tggaatcaacgagaatgattttgaaccatagtattaacaaagctgcaattgataaatgtggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACGATCTCA

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------------gtatatctgcaaggctctagtttt-atgttcccttcatctttttaaaattctttctctatcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG
                                                                     |  ||    ||||   ||||||| |  ||  | |    ||  || || |     |||||       |||| || ||||||||||||||||| || || |||||||||||  | || || |||||||||||||| |||||||||||||| || ||||| ||| | 
gtttgtttactaggcttaagttattttggtagatgcttgcagttgatagccctctagtgcccaggactattaatggaaaaggtattagtttttaaattatcatgtaattgatagaaattaacttctat-------agGTTGGGACAATATCAGCAAATGGTGAGAGAGAAATTGGTGAATTGATCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------------------------------------------------------------------------gtatatctgcaaggctctagttttatgttcccttcatctttttaaaattctttctctatcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG
                                                                                                                   | | | ||||     |    || | |  |    ||| ||   || ||| ||   | | | |||  | ||| || || || || |||||||| || || |||||||| ||  |  | ||    || ||||||||||||||||| || |||||||||||| |  ||
gtgagtactctttcgctaaattcaccatttcaaggtgatgcatacttcgatttgaggtttttgtactgcgggattcaagataattggaccatttcctcatttgtgtgggcgtggtggagagctgcgca-ttgcgattgtttaattaaatca-ctccatacaatcctccgttt-ttctgcca-gGTTGGAACTATCTCTGCAAATGGAGATAGTGAAATTGGCGATTTGCTCGCTCGCGCCATGGAGAAGGTTGGCAAGGAAGGTGTCATCACTGTGTCG

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------gtatatctgcaaggctctagttttatgttcccttca----tctttttaaaattctttctc-tatcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG
                                                                                     | | |   | | |||     |  | ||  | |  |    || ||      || | | |  | | |||  | ||| || ||||| || || ||||| ||  | |||||||||||  |  | ||    |||||||||||||||||||| ||||||||||||||| |  | 
gtaagcaaatcaccatctgaaggtgatactagaattttagcatcttgtttttgggcttaaactctaatatagaaaatctcgtggatgtgttgccgaagctactaatggaagtcacttcaacggatcattccttgcttttgtgtggtgttctgcca-gGTTGGAACAATCTCTGCGAATGGAGACCGAGAAATTGGTGACTTGCTAGCTCGTGCTATGGAGAAGGTTGGCAAGGAGGGTGTCATCACTGTCTCT

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ20894 (Selaginella moellendorffii), 3'ss of exon 3
gtatatctgca-aggctctagttttatgttcccttcatctttttaaaattctttctctatcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG
     ||||   || || | | ||| || |  | | | |||||                    ||| |||| ||||| || || |||||||| || |||||||| ||||| || ||||| |  || ||||||||||| |||||||| |||||||||||  |  ||
----gtctgagcagccttttggtttgtgcttaccttagcttttcggtg--------------cgtgcagGTCGGTACCATTTCGGCAAATGGTGACAGGGAAATCGGTGACCTGATTGCTAGAGCCATGGAGAAGGTCGGCAAAGATGGTGTCATCACAGTATCG

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ32351 (Selaginella moellendorffii), 3'ss of exon 3
gtatatctgcaaggctctagttttatgttcccttcatctttttaaaattctttctctatcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG
     ||||    ||  |  || | | ||   ||  | |  |||   | |||| ||  | | ||| |||| ||||| || || |||||||| || |||||||| ||||| || ||||| |  || ||||||||||| |||||||| |||||||||||  |  ||
----gtctgagcagcctt--ttctgtattgagttt-tatgcttacgttactttttcggtgc-gtgcagGTCGGTACCATTTCGGCAAATGGTGACAGGGAAATCGGTGACCTGATTGCTAGAGCCATGGAGAAGGTCGGCAAAGATGGTGTCATCACAGTATCG

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|33101516|gb|CF061476.1|CF061476
EST:     ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCGGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
EST: gi|31355867|gb|CD440224.1|CD440224
EST:     ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCACCAAATGGGGAAAGGGAAAT
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAAT
EST: gi|33102191|gb|CF062151.1|CF062151
EST:     ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCGGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
EST: gi|31357599|gb|CD441956.1|CD441956
EST:     ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
EST: gi|61119163|gb|DN560124.1|DN560124
EST:     ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
EST: gi|13388799|gb|BG462407.1|BG462407
EST:     ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
EST: gi|31361464|gb|CD445821.1|CD445821
EST:     ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
EST: gi|88747169|gb|DY531310.1|DY531310
EST:     ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
EST: gi|5499101|gb|AI854968.1|AI854968
EST:     ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
EST: gi|31441079|gb|CD510510.1|CD510510
EST:     ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCAGCAAATGGGGAA
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAA
EST: gi|31349389|gb|CD433746.1|CD433746
EST:     ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
EST: gi|67016113|gb|CO444862.1|CO444862
EST:     ATCTGAAA-GCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
EST: gi|94476466|gb|EB705424.1|EB705424
EST:     ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
EST: gi|67023196|gb|CO451945.1|CO451945
EST:     ATCTGAAAGGCGTGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
EST: gi|31355665|gb|CD440022.1|CD440022
EST:     ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAG                         GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC
genomic: ATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCC

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), 48 (downstream exon)
Score: 374

AATGGATTTAAGGCGCGGAATCTCAATGGCTGTTGACGCTGTTGTGACCAATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 220

AATGGATTTAAGGCGCGGAATCTCAATGGCTGTTGACGCTGTTGTGACCAATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 175

AATGGATTTAAGGCGCGGAATCTCAATGGCTGTTGACGCTGTTGTGACCAATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 287

AATGGATTTAAGGCGCGGAATCTCAATGGCTGTTGACGCTGTTGTGACCAATCTGAAAGGCATGGCCAGAATGATCAGCACTTCAGAAGAAATTGCACAGgtatatctgc ... tcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctctagttttatgttcccttcatctttttaaaattctttctctatcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG
                                  ttctttctctatcctg  CT-rich tract
                   ttcatctttttaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatctgcaaggctctagttttatgttcccttcatctttttaaaattctttctctatcctgtgaagGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG