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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctccctctggcctccttttctgtttgatcacatatgcacttgttcccccatggttcttggtttccttcagatctggtgcttgtgtcatcggtttcctcaattgtctggcatctgcattgactcatgatgggtgatgctatgctgtgttctgtggtgtttgtctcag

Basic information

species Zea mays
transcript GRMZM2G154890_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154890_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g22140.1 (Oryza sativa), 5'ss of exon 2
TGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctccctctggcctccttttctgtttgatcacatatgcacttgt-tcccccatggttcttggtttccttcagatctggtgcttgtgtcatcggtttcctcaattgtctggcatctgcattgactcatgatgggtgatgctatgctgtgt-tctgtggtgtttgtctcag
 |    |  |      || |  |  |  |  ||    |||||||| |||||||| ||||| ||||||||||||||||||||||||||||||||||||||||||||||  ||| |   || ||      ||||     | | |||  || | |   | ||  ||||   |    |   ||||||| ||||| |   |  ||| |            | |  |   |||| |  |  ||  ||||||| |   | |  ||| |||  |    | |||
CGGGGGCGGCGAAGAGTCCCGTGAGCGCCTCCTAG--ATGGGGCTGCTCAGCATCATCCGGAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggtgcccccct-ccacccccagagttt-----cttttgcgattctgtgggcaatccttctctctccattctggatctggcgcttgagcggttcgttcctct---------gtagatttcttgattttttgtgcctgatgctgtctggggaatctatgggttcacccgcag

upper sequence: GRMZM2G154890_T03 (Zea mays), 5'ss of exon 2
lower sequence: PP1S62_133V6.2 (Physcomitrella patens), 5'ss of exon 1
TGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctccctctggcctccttttctgtttgatcacatatgcacttgttcccccatggttcttggtt--tccttcagatctggtgcttgtgtcatcggtttcctcaattgtctggcatctgcattgactcatgatgggtgatgctatgctgtgttctgtggtgtttgtctcag
   | | |   |      |  |        |  |||||||||| | || |  || ||| | ||  | ||||| ||||||||||||||||| ||| |||||||||| |     ||    || || ||     |  | |    ||  | ||||| |   | | |   ||||  |  ||||  ||||||  |  |||| ||   || |||| |||       | |||  ||  |  |||||   || | | |  ||||| |    |            
--TAACTCGGATTGAAATTTGCAAGAAGGTATCGATCATGGGGTTGCTGACGATCATCAGGAAAGTGAAGCGGAAGGAGAAGGAGATGCGGATCTTCATGGTgtatgtgt--tcaactctgctgtttcagcttgtgatcggtgtccctgttctc---taggttcgggttgataattcatttctggt--tgatgtcttca--tttctcagttg------gtatgctgtgggtt-tgatgta-gacgtt-tcttgtgtgcctcag------------

upper sequence: GRMZM2G154890_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ26161 (Selaginella moellendorffii), 5'ss of exon 1
TGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctccctctggcctccttttctgtttgatcacatatgcacttgttcccccatg-gttcttggtttccttcagatctggtgcttgtgtcatcggtttcctcaattgtctggcatctgcattgactcatgatgggtgatgctatgctgtgttctgtggtgtttgtctcag
                                     |||||||| ||||  || ||||||||| | ||||||||||||||||| |||||||| ||||||||||| |||| ||||  |   || |     | ||||     |||  |  |    || || |   ||| |||||  |  |                                                                                               
-------------------------------------ATGGGGCTGCTCACGATCATCCGCAAGGTGAAGCGCAAGGAGAAGGAAATGCGCATTCTCATGGTgtaagctctctct--ctctctctctctctcgatctttcttgcggtgctatgtccttgcgcatttgatttccgccgcag----------------------------------------------------------------------------------------------

upper sequence: GRMZM2G154890_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ10782 (Selaginella moellendorffii), 5'ss of exon 1
TGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctccctctggcctccttttctgtttgatcacatatgcacttgttcccccatggttcttggtttccttcagatctggtgcttgtgtcatcggtttcctcaattgtctggcatctgcattgactcatgatgggtgatgctatgctgtgttctgtggtgtttgtctcag
                                     |||||||| ||||  || ||||||||| | ||||||||||||||||| |||||||| ||||||||||| |||| ||||   |||  | ||  | |     |||  |    | |  ||    |    ||| |||||  |  |                                                                                               
-------------------------------------ATGGGGCTGCTCACGATCATCCGCAAGGTGAAGCGCAAGGAGAAGGAAATGCGCATTCTCATGGTgtaagctctctct---ctctctctcgatct---ttcatgcggtgctatgtccttgcg-catttgatttccgccgcag----------------------------------------------------------------------------------------------

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|34391377|gb|CF384605.1|CF384605
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|34391377|gb|CF384605.1|CF384605
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|91874746|gb|EB404703.1|EB404703
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|91874746|gb|EB404703.1|EB404703
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|89755818|gb|DY686096.1|DY686096
EST:     CATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCCATCCTCATG                         G
genomic: CATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGC-ATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|89755818|gb|DY686096.1|DY686096
EST:     CATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCCATCCTCATG                         G
genomic: CATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGC-ATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|78112616|gb|DV531010.1|DV531010
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|78112616|gb|DV531010.1|DV531010
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|50339681|gb|CO534807.1|CO534807
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|50339681|gb|CO534807.1|CO534807
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|78114767|gb|DV533155.1|DV533155
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGG                         T
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCAT-Ggtgtaggctc ... tttgtctcag-
EST: gi|78114767|gb|DV533155.1|DV533155
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGG                         T
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCAT-Ggtgtaggctc ... tttgtctcag-
EST: gi|211104769|gb|FL158955.1|FL158955
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|211104769|gb|FL158955.1|FL158955
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|5932640|gb|AW057001.1|AW057001
EST:     ATCCTCATGGT                         TGGCCTGGACAACTCAGGGAAGACAACCATCGTTCTCAAGATCAATGGGG
genomic: ATCCTCAT-G-gtgtaggctc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGG
EST: gi|91875540|gb|EB405497.1|EB405497
EST:     ATCCTCATGGT                         TGGCCTGGACAACTCAGGGAAGACAACCATCGTTCTCAAGATCAATGGGG
genomic: ATCCTCAT-G-gtgtaggctc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGG
EST: gi|91875540|gb|EB405497.1|EB405497
EST:     ATCCTCATGGT                         TGGCCTGGACAACTCAGGGAAGACAACCATCGTTCTCAAGATCAATGGGG
genomic: ATCCTCAT-G-gtgtaggctc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGG
EST: gi|60337602|gb|DN204575.1|DN204575
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGG                         T
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCAT-Ggtgtaggctc ... tttgtctcag-
EST: gi|60337602|gb|DN204575.1|DN204575
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGG                         T
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCAT-Ggtgtaggctc ... tttgtctcag-
EST: gi|50335743|gb|CO530869.1|CO530869
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         TGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|76016499|gb|DT943669.1|DT943669
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|76016499|gb|DT943669.1|DT943669
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|86469538|gb|DY235908.1|DY235908
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|86469538|gb|DY235908.1|DY235908
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|89248462|gb|DY620248.1|DY620248
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|89248462|gb|DY620248.1|DY620248
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|76286526|gb|DV026094.1|DV026094
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|76286526|gb|DV026094.1|DV026094
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|74239326|gb|DT647240.1|DT647240
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|74239326|gb|DT647240.1|DT647240
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|71318964|gb|DR796231.1|DR796231
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|71318964|gb|DR796231.1|DR796231
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|78082479|gb|DV510891.1|DV510891
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-
EST: gi|78082479|gb|DV510891.1|DV510891
EST:     GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG                         G
genomic: GCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcag-

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 3 RNA-Seq libraries.


Block sizes: 40 (upstream exon), 18 (downstream exon)
Score: 6

TGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGAGGACACCAGCATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATC


Block sizes: 45 (upstream exon), 44 (downstream exon)
Score: 9

TGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGAGGACACCAGCATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 6

TGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGAGGACACCAGCATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGgtgtaggctccctctggcctccttttctgtttgatcacatatgcacttgttcccccatggttcttggtttccttcagatctggtgcttgtgtcatcggtttcctcaattgtctggcatctgcattgactcatgatgggtgatgctatgctgtgttctgtggtgtttgtctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG