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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcactggagtgcattggtgtccatgcttcctttaactgcttttatttaaacttttctgtacctaggagtgcagtgacttcgtgtttgtgttaca...

Basic information

species Zea mays
transcript GRMZM2G100872_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 1
TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaattt----cactggagtgcattggtgtccatgcttcctttaactgcttttatttaaacttttctgtacctaggagtgcagtgacttcgtgtttgtgttaca
|||| || |||||||| || || |||||||||||||||||||||||||| || |||||||| || ||||| |||||||||||||| |||||||| ||||||| ||||    ||||||       ||           | || || |  || | |  | | ||   | |     | |  | |  |    | || ||||   ||  
TCTGCGTGTACTGCCCCGGAGGCCCCGACTCCGACTTCGAGTACAGCACCCAGTCCTACACCGGCTACGAGCCCACCAGCATGCGCGCCATTCGAGCAAGgtgatttacctcactggctactgatgtcacttggaaatactataccacctgtgagatgagctgcacggcg---atgctttctctagtgttgt-tttgaagtatg

upper sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA06G18150.1 (Glycine max), 5'ss of exon 1
TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcactggagtgcattggtgtccatgcttcctttaactgcttttatttaaacttttctgtacctaggagtgcagtgacttcgtgt-ttgtgttaca---
|||| ||||||||||| || || || |||||||||||||||||||| || || || ||||| || || ||||| ||||||||||||||  |||| || |||||   |   ||    |  |||   |   || |    | |||     |  ||| ||      || |     ||||  | | | | | | | || ||||      
TCTGCGTCTACTGCCCCGGGGGACCTGACTCCGACTTCGAGTACAGTACCCAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAGgtagggtttatgtta-gttttgtcttttgtgttagggtaaacgaaactgtttttaagag---tgaatagttgagtcaaattaatccctatattctgttgatttt

upper sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA04G36790.1 (Glycine max), 5'ss of exon 1
TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcactggagtgcattggtgtccatgcttcctttaactgcttttatttaaacttttctgtacctaggagtgcagtgacttcgtgt-ttgtgttaca---
|||| ||||||||||| || || || |||||||| ||||||||||| || || || |||||||| |||||||| ||||||||||| || ||||| || |||||   |   ||    |  |||   ||  || |    | ||  |   | |||| ||      || |     ||||  | | | | | | | || ||||      
TCTGCGTCTACTGCCCCGGGGGACCTGACTCCGATTTCGAGTACAGTACTCAGTCTTACACTGGTTACGAACCAACCAGCATGCGCGCAATTCGTGCGAGgtagggtttatgtta-gttttgtcttctgtgttagggtaaatggaactgattttaagag---tgaatagttgagtcaaattaatccctatattctgttgatttt

upper sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 5'ss of exon 1
TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaa--tttcactggagtgcattggtgtccatgcttcctttaactgcttttatttaaacttttctgtacctaggagtgcagtgacttcgtgtttgtgttaca---
| ||||| || ||||| || || || || || || || |||||||| || || || |||||||||||||| |||||||||||||| || ||||| || |||||   |||  ||  || |  ||  | |   |  ||  | ||      | | |||  | |  |  | |   |   |   ||  |||  || |||   |||     
TTTGTGTTTATTGCCCTGGAGGACCTGATTCTGATTTTGAGTACAGTACACAGTCGTACACTGGATACGAGCCCACCAGCATGCGCGCGATTCGTGCTAGgtagggtttttctttag-gttttaattt---tatttgttgtattgatctctgtttgga-tgatgggaaatcataggaaaaggaactaagtcttttcattaatgaa

upper sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 1
lower sequence: EDO97260 (Chlamydomonas reinhardtii), 5'ss of exon 5
TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcactggagtgcattggtgtccatgcttcctttaactgcttttatttaaacttttctgtacctaggagtgcagtgacttcgtgtttgtgttaca-------------------------
                     | |||||||| ||||| ||||||||||| || || ||||| || ||||| |||||||||||| | ||||| |||||  ||||    |  |   |||||     |  | |||    |    ||       | ||  | |      | |  || | | ||||     ||||  | |  ||                          
---------------------GCCCCGACTCGGACTTTGAGTACAGCACTCAGTCGTACACGGGGTACGAGCCCACCAGCATGAGGGCCATACGGGCGCGGTACGACCCGTAC-GTGCAGgtacgggcgtgcggagtacggcttggggggtgtagccgtcc----atccggggg-gtagtggtcgtgtgtgagggcaacgggttctgcgggcgctggtgggggca

upper sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S185_41V6.1 (Physcomitrella patens), 5'ss of exon 2
TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcactggagtgcattggtgtccatgcttcctttaact--gcttttatttaaacttttctgtacctaggagtgcagtgacttcgtgtttgtgttaca-----
| ||||| |||||||| || || || ||||| || || || ||||| || ||||| |||||||| |||||||| ||||||||||| ||||| ||||| |||||        |   || ||| |   | ||      || |  |  ||   | ||| |  |||  | | |   |  || ||   | |    ||||   | ||      
TTTGTGTTTACTGCCCTGGAGGGCCGGACTCTGATTTTGAATACAGTACTCAATCATACACTGGTTACGAACCTACCAGCATGCGAGCCATCCGGGCGAGgta------tggatttgtattcgaacctataaccttttcacttttgcagctttttgatttttattctcctatgacgtccacctaatcta-gtttcattaactgagga

upper sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ27096 (Selaginella moellendorffii), 5'ss of exon 1
------------------------------------TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcactggagtgcattggtgtccatgcttcctttaactgcttttatttaaacttttctgtacctaggagtgcagtgacttcgtgtttgtgttaca
                                    ||||||||| ||||||||| || || || || |||||| | || ||||| || ||||||||||| || ||||| || |||||| | || ||||| ||||||||| ||        |  | |  | | |||   | ||||   ||||   |   |||||                                          
CATGTCCAAGCCGCATCGGTGCCCACACATCGCCTATCTGTGTCTGCTGCCCGGGAGGCCCAGATTCGGACTTCAAATATAGCACACAGTCCTACACTGGgtatgaaccaacgagcatgagagcaattcgagcaaggtaaatt-------atatagtctttttcat---ttctttttttgctagaaaaaaaactcag---------------------------------------

upper sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ21486 (Selaginella moellendorffii), 5'ss of exon 1
TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcactggagtgcattggtgtccatgcttcctttaactgcttttatttaaacttttctgtacctaggagtgcagtgacttcgtgtttgtgttaca
||||||||||||||||||| || || || || |||||||| || ||||| || ||||||||||| || ||||| || |||||||| || ||||| ||||||||| |||       |  | |  | | |||   | ||||   ||||   |   |||  ||                                        
TCTGTGTCTACTGCCCGGGAGGCCCAGATTCGGACTTCGAATATAGCACACAGTCCTACACTGGGTATGAACCAACGAGCATGCGAGCAATTCGAGCAAGgtaaattc-------tatagtctttttcat---ttctttttttgctagcaaaaaaaaattcag-------------------------------------

upper sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ27088 (Selaginella moellendorffii), 5'ss of exon 1
TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcactggagtgcattggtgtccatgcttcctttaactgcttttatttaaacttttctgtacctaggagtgcagtgacttcgtgtttgtgttaca
||||||||||||||||||| || || || || |||||||| || ||||| || ||||||||||| || ||||| || |||||| | || ||||| ||||||||| |||       |  | |  | | |||   | ||||   ||||   |   |||  ||                                        
TCTGTGTCTACTGCCCGGGAGGCCCAGATTCGGACTTCGAATATAGCACACAGTCCTACACTGGGTATGAACCAACGAGCATGAGAGCAATTCGAGCAAGgtaaattc-------tatagtccttttcat---ttctttttttgctagcaaaaaaaaattcag-------------------------------------

upper sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ27078 (Selaginella moellendorffii), 5'ss of exon 1
TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcactggagtgcattggtgtccatgcttcctttaactgcttttatttaaacttttctgtacctaggagtgcagtgacttcgtgtttgtgttaca
||||||||||||||||||| || || || || |||||||| || ||||| || ||||||||||| || ||||| || |||||||| || ||||| ||||||||| |||       |  | |  | | |||   |  |||  ||      |   |||                                            
TCTGTGTCTACTGCCCGGGAGGCCCAGATTCGGACTTCGAATATAGCACACAGTCCTACACTGGGTATGAACCAACGAGCATGCGAGCAATTCGAGCAAGgtaaattc-------tatagtctttttcatttctttttttgctagcaaaaaaaaaatcag----------------------------------------

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|76923552|gb|DV169543.1|DV169543
EST:     CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAG                         GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
genomic: CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
EST: gi|211469955|gb|FL098251.1|FL098251
EST:     CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAG                         GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
genomic: CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
EST: gi|50328156|gb|CO523282.1|CO523282
EST:     CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAG                         GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
genomic: CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
EST: gi|78112309|gb|DV530703.1|DV530703
EST:     CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAG                         GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
genomic: CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
EST: gi|93283964|gb|EB676228.1|EB676228
EST:     CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAG                         GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCT
genomic: CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCT
EST: gi|148941357|gb|EC886266.2|EC886266
EST:     CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAG                         GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
genomic: CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
EST: gi|149001061|gb|EE038313.2|EE038313
EST:     CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAG                         GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
genomic: CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
EST: gi|91049795|gb|EB160213.1|EB160213
EST:     CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAG                         GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
genomic: CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
EST: gi|148940806|gb|EC885631.2|EC885631
EST:     CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAG                         GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
genomic: CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
EST: gi|89253138|gb|DY624924.1|DY624924
EST:     CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAG                         GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
genomic: CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
EST: gi|78119531|gb|DV537915.1|DV537915
EST:     CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAG                         GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
genomic: CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
EST: gi|50330596|gb|CO525722.1|CO525722
EST:     CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAG                         GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT
genomic: CAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTT

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), 47 (downstream exon)
Score: 59

TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 38

TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 34

TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG


Block sizes: 36 (upstream exon), 45 (downstream exon)
Score: 46

TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcac ... tacattctagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG