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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAAGGTTCTCACACCATACTCTTCAGAAGATGCCCGAGGCTTGCTTAAAGCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagtctgatcttgttgaatcattttgctagctgcctatcattttgctgagatgctattgtaccatttgcag

Basic information

species Zea mays
transcript GRMZM2G128121_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128121_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 8
TTAAGGTTCTCACACCATACTCTTCAGAAGATGCCCGAGGCTTGCTTAAAGCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagtctgatcttgttgaatcattttgctagctgcctatcattttgctgagatgctattgtaccatttgcag---
||||||||||    ||||| ||| |||||||||| || |||||||| |||||||| ||||||||||| || |||||| ||||||||||||||||| |||||||||  |   ||||||||||     ||    ||  ||  |  ||||||  |  |||||||  | ||| |||| | |   
TTAAGGTTCTGGTTCCATATTCTGCAGAAGATGCTCGTGGCTTGCTCAAAGCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatgg-aacatgatcttgttatgctat---actgactagccgtcatttccccaagatgctgatatactattttctgcag

upper sequence: GRMZM2G128121_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA14G02380.2 (Glycine max), 5'ss of exon 8
TTAAGGTTCTCACACCATACTCTTCAGAAGATGCCCGAGGCTTGCTTAAAGCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagtctgatcttgttgaatcattttgctagctgcctatcattttgctgagatgctattgtaccatttgcag----------------------------------------------------------------
| || ||  |  ||||||| || || |||||||| || || ||||||||||||||||| ||||| |||||||||||| ||||| | |||||||||||| |||| ||    |||  |||| |    |        |   | |  |  |  ||||    |  ||    |  ||  |  |                                                                
TGAAAGTCTTGTCACCATATTCATCTGAAGATGCTCGTGGTTTGCTTAAAGCTGCTATAAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtgctg--cttgattctcccaccccaaaaaagacacttgtgctgcttgatttgtacatgaaaatgagtggtcatagattttgacatcagttcttgtttcaaaaaatatttaatttgatggattatgtcctctag

upper sequence: GRMZM2G128121_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 8
TTAAGGTTCTCACACCATACTCTTCAGAAGATGCCCGAGGCTTGCTTAAAGCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagtctgatcttgttgaatcattttgctagctgcctatcattttgctgagatgctattgtaccatttgcag----------------------------------------------------------------
| || ||  |  ||||||| || || |||||||| || || ||||||||||||||||| ||||| |||||||||||| ||||| | |||||||||||| |||| ||    |||  |||| |    |        |   | || |  |  ||||    |  ||    |  ||  | ||                                                                
TGAAAGTCTTGTCACCATATTCATCTGAAGATGCTCGTGGTTTGCTTAAAGCTGCTATAAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtgctg--cttgattctcccgccccaaaaaagactcttttgctgcttgatttgtacatgaaaatgagtagtcatagattttggcatcagttcttgtttcaaaaaatatttaatttgatgaattatgtcctctag

upper sequence: GRMZM2G128121_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA14G36540.3 (Glycine max), 5'ss of exon 8
TTAAGGTTCTCACACCATACTCTTCAGAAGATGCCCGAGGCTTGCTTAAAGCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagtctgatcttgttgaatcattttgctagctgcctatc-attttgctg--agatgctattgtaccatttgcag------------------------
| || ||  |  ||||||| || || ||||||||||| || ||||||||||||||||||||||| |||||||||||| ||||| | |||||||||||| |||| ||    ||| | | |||   ||||     |   |    ||  ||||||     || |  | ||  |  || |                            
TGAAAGTCTTGTCACCATATTCATCTGAAGATGCCCGTGGTTTGCTTAAAGCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtgctgct-tggtttgttcatgaaaatgagtagtcatagattttgacatcagttcttgtttcaaaatatatttaatttcatgaattatgtcctctag

upper sequence: GRMZM2G128121_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 5'ss of exon 8
TTAAGGTTCTCACACCATACTCTTCAGAAGATGCCCGAGGCTTGCTTAAAGCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagtctgatcttgttgaatcattttgctagctgcctatcat---tttgctgagatgcta-ttgtaccatttgcag---
| ||||| ||    ||||| || ||||| || || || ||| || | ||||||||||| ||||| ||||| |||||| ||||| | ||||| |||||||||| |     | ||||  | |   ||   | ||  |   |   ||  |    || || |      | ||| |     ||| |   
TGAAGGTGCTGGTTCCATATTCATCAGAGGACGCTCGGGGCCTGTTAAAAGCTGCTATAAGGGACCCTGACCCTGTTGTTTTCCTTGAAAACGAATTGCTgt-tagtgttttgatgct-tgagatttctctgtaattggatcattgtatacttactcatccttgagttgaatttcatgctgcag

upper sequence: GRMZM2G128121_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 5'ss of exon 9
TTAAGGTTCTCACACCATACTCTTCAGAAGATGCCCGAGGCTTGCTTAAAGCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagtctgatcttgttgaat-cattttgctagctgcctatcattttgc-tgagatgctattgtaccatttgcag------------
| || || ||  | ||||| || || || |||||||| || ||||| ||||||||||| || || |||||||||||||||||| | |||||||| |||||||| |||        |    ||  |  | | || ||  |  || ||||||    |   |   | || | | |  || |             
TGAAAGTGCTGTCCCCATATTCATCTGAGGATGCCCGTGGATTGCTAAAAGCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtcaattgcaaagtggttgtactatgttatgtttct-tcatttcatatttaacattgttatccaacctgaactttgtgcttcag

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|78104220|gb|DV522638.1|DV522638
EST:     GCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: GCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
EST: gi|71325375|gb|DR799361.1|DR799361
EST:     GCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: GCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
EST: gi|211386006|gb|FL329690.1|FL329690
EST:     GCTGCTATTAGGGATCCCGATCCTGTTATTTTCTTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: GCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
EST: gi|211417439|gb|FL345693.1|FL345693
EST:     TTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: TTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
EST: gi|78081841|gb|DV510253.1|DV510253
EST:     GGATCCTGATCCTGTTATTTTC-TGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: GGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
EST: gi|78180140|gb|DV550513.1|DV550513
EST:     GCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: GCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
EST: gi|12045820|gb|BF727959.1|BF727959
EST:     GCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: GCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
EST: gi|31348876|gb|CD433233.1|CD433233
EST:     GCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: GCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
EST: gi|6859967|gb|AW355961.1|AW355961
EST:     GCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: GCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG

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: 122

TTAAGGTTCTCACACCATACTCTTCAGAAGATGCCCGAGGCTTGCTTAAAGCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 172

TTAAGGTTCTCACACCATACTCTTCAGAAGATGCCCGAGGCTTGCTTAAAGCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

TTAAGGTTCTCACACCATACTCTTCAGAAGATGCCCGAGGCTTGCTTAAAGCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 389

TTAAGGTTCTCACACCATACTCTTCAGAAGATGCCCGAGGCTTGCTTAAAGCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAAGGTTCTCACACCATACTCTTCAGAAGATGCCCGAGGCTTGCTTAAAGCTGCTATTAGGGATCCTGATCCTGTTATTTTCTTGGAAAATGAATTGCTgtatgtcagtctgatcttgttgaatcattttgctagctgcctatcattttgctgagatgctattgtaccatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT