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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactattcttcttgtatgcttttccttcagttaagcgattggtactgacacctgttattgcctgttaactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG

Basic information

species Zea mays
transcript GRMZM2G096343_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 3'ss of exon 9
gtaactattct-tcttg-----tatgcttttccttcagttaagcga-------ttggtactgacacctgttattgcctgttaactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG
|||| |||| |  | ||     |||||||  | |  |||   | |        ||  ||   |  | || | ||      | |   |||||| || || |  || ||  ||||| ||||||||||||||||||| |||||||||||||||||||||| ||| ||||| |||||||||||||||
gtaattattgtgccctgctgcttatgcttaccatatagtggggagtggggacttttataacaattcttgctctttttccatcatgatcagGTCGGATCTGTTCTTCTCAGTTGTTCCTTCTTATATGACATCTTTTGGGTTTTTATCTCCAAGATGTGGTTTCATGAGAGTGTGATGATTGTG

upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G07610.1 (Glycine max), 3'ss of exon 10
-------------------gtaactattct------tcttgtatgcttttccttcagttaagcgattggt-actgacacctgttattgcctgttaactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG
                    || || | ||      |  || |   || |  |  |   || |   |  | |||||||  |   |||  || | ||   |||||| ||  | |  || ||  ||||||||||| ||||||||||||||||||| ||| |||| ||   || ||||||||| ||||||||||| |||
ctgacagatcgttgaagagatagctttgctggatactactgaacttttattatgaacaaaaacacctactgactgacatataccattttctctgaa---tcagGTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATATGACATCTTCTGGGTGTTTGTCTCTAAACGGTGGTTCCATGAGAGTGTGATGATAGTG

upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 9
--------------------------------------------------------------------------------------------------------------------gtaactattcttcttgtatgcttttccttcagttaagcgattggtactgacacctgttattgcctgttaac--tgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG
                                                                                                                     ||| |||   |||  | | || || ||    ||      |    |   ||||   ||  | | | ||  |  ||| |||| ||  | |  || ||  ||||||||||| |||| |||||||||||||| ||| |||| ||   || ||||||||| ||||||||||| |||
gtgattatacattacttaagcttgtattttgcacaatcacctacttaggttgtttgttatattcttgaaaattaagcttgggatgcataaaggggacctccatatcagtgaaacatttaaatatggatctactgt-ctattactgaccttttttattaacaaaaaacactaatttatacattttttccatgtaagGTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATACGACATCTTCTGGGTGTTTGTCTCTAAATGGTGGTTCCATGAGAGTGTGATGATAGTG

upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA18G46760.1 (Glycine max), 3'ss of exon 9
----------------------gtaactattcttcttgtatgcttttcct-tcagttaagcgattggtactgacacctgttattgcctgttaactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG
                       ||| |||   |||    ||  || |    || ||     |     |  |||   | |       | ||   ||| |||| ||  | |  || ||  ||||||||||| |||| |||||||||||||| ||| |||| ||   || ||||||||| ||||||||||| |||
tttttatatttcagtgaaacgattaaatatggatctacagtgtattactgaccatttttattaacaaaaaagactaatttatacattttttccatgtaagGTCGGAACTGTTCTTCTCAGTTGTGCCTTCCTATACGACATCTTCTGGGTGTTTGTCTCTAAATGGTGGTTCCATGAGAGTGTGATGATAGTG

upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA03G01100.1 (Glycine max), 3'ss of exon 9
-----------------gtaactattctt----cttgtatgcttttccttcagttaagcgattggt-actgacacctgt-tattgcctgttaactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG
                  || || | ||     ||  |   |||||  |      ||   |      ||||||     | ||     | ||     |||||| ||  | |  || ||  ||||||||||| |||||||||| || ||||| ||| |||| ||   || ||||||||| ||||||||||| |||
gacaaatcattgaagacatagctttgctggatactactgaacttttattatgaacaaaaaagcacccactgaccgacatatacctttttttctgaatcagGTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATATGACATTTTTTGGGTGTTTGTCTCTAAACGGTGGTTCCATGAGAGTGTGATGATAGTG

upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G63690.2 (Arabidopsis thaliana), 3'ss of exon 9
--------------gtaactattcttcttgtatgcttttccttcagttaagcgattggtactgacacctgttattgcctgttaactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG----
              |||  ||| | || |    |  |||||   | ||     |    ||   |  |   ||||  | ||  |     ||||| ||  |||  || ||  | ||||||||||| || || ||||||||||| ||| ||||||||| ||||||||| ||||| || ||||||||     
gtaatttcttgaacgtatttatacgtcatcgtagagtttccaaaactttttgaaagattataaagccacattatcacttgaaa-----cagGTCGGGACAGTTCTTCTCAGCTGTGCCTTCTTGTACGATATCTTCTGGGTGTTTGTCTCCAAGAAGTTGTTCCACGAAAGCGTAATGATTGTCGTAA

upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G63690.1 (Arabidopsis thaliana), 3'ss of exon 9
--------------gtaactattcttcttgtatgcttttccttcagttaagcgattggtactgacacctgttattgcctgttaactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG
              |||  ||| | || |    |  |||||   | ||     |    ||   |  |   ||||  | ||  |     ||||| ||  |||  || ||  | ||||||||||| || || ||||||||||| ||| ||||||||| ||||||||| ||||| || |||||||| 
gtaatttcttgaacgtatttatacgtcatcgtagagtttccaaaactttttgaaagattataaagccacattatcacttgaaa-----cagGTCGGGACAGTTCTTCTCAGCTGTGCCTTCTTGTACGATATCTTCTGGGTGTTTGTCTCCAAGAAGTTGTTCCACGAAAGCGTAATGATTGTC

upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 9
--------------gtaactattcttct---tgtatg------cttttccttcagttaagcgattggtactgacacctgttattgcctgttaactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG
                ||  |||  |     |||||       |  |  ||  | | |    ||| ||  |||   ||  |    |   |       ||||| || |  |  || ||  | ||||||||| | ||||||||||||||||||||| | || ||   || ||||| |||||| ||||||||||||
gctggtagacggatacaatcatttctgccaatgtatagaagaccaatctctataataacaatattagttatgatgactcattgaactcttacgtaaacagGTCGGGTTTGTTCTTCTCAGCTGTGCCTTCATGTATGACATCTTCTGGGTTTTTGTTTCAAAATGGTGGTTCCGTGAAAGCGTGATGATTGTG

upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv02s0025g03400.t01 (Vitis vinifera), 3'ss of exon 9
-------------------------gtaactattcttcttgtatgcttttccttcagttaagcgattggtactgacacctgttattgcctgttaactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG
                          | | ||||    |  ||| | |  |   ||  | |  | |   | |||||| | |||   |  | ||     |||||||||| |||  || ||  |||||||||| || || |||||||| ||||| ||  | || || | | ||||||||||||||||||||||||||
caagttatagatgaaatggttcaagatcaatattacaatgatatccctggctagcaaatgattgttc--ttctgacagcagtttgagtgttttgtgaatcagGTGGGTACAGTTCTTCTTAGTTGTGCCTTTTTGTACGACATCTTTTGGGTGTTCGTTTCTAAAAAGCTGTTCCATGAAAGTGTGATGATTGTG

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|60344430|gb|DN211403.1|DN211403
EST:     TTACCTTGATCGTTACAGTCATCCAAATTGTTAGAATACCTAACCTTAAG                         GTGGGTTCAGCCTTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTT
genomic: TTACCTTGATCGTTACAGTCATCCAAATTGTTAGAATACCTAACCTTAAGgtaactattc ... taactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTT
EST: gi|67041082|gb|CO467337.1|CO467337
EST:     TTACCTTGATCGTTACAGTCATCCAAATTGTTATAATACCTAACCTTAAG                         GTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTT
genomic: TTACCTTGATCGTTACAGTCATCCAAATTGTTAGAATACCTAACCTTAAGgtaactattc ... taactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTT

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: 164

GGTATTACCTTGATCGTTACAGTCATCCAAATTGTTAGAATACCTAACCTTAAGgtaactattc ... taactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG


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

GGTATTACCTTGATCGTTACAGTCATCCAAATTGTTAGAATACCTAACCTTAAGgtaactattc ... taactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 289

GGTATTACCTTGATCGTTACAGTCATCCAAATTGTTAGAATACCTAACCTTAAGgtaactattc ... taactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

GGTATTACCTTGATCGTTACAGTCATCCAAATTGTTAGAATACCTAACCTTAAGgtaactattc ... taactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccttcagttaagcgattggtactgacacctgttattgcctgttaactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG
                                tgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactattcttcttgtatgcttttccttcagttaagcgattggtactgacacctgttattgcctgttaactgtcagGTGGGTTCAGCCCTCCTGGGTTGTGCCTTCTTATATGACATCTTCTGGGTTTTTATCTCCAAGATGTTGTTCCATGAAAGTGTGATGATTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG