Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatatatttttttctctttttttgcttgctatatccctttgagctcaactatcctatccaataaaatctcagttctgcatgcactgatattatgttttgttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTTTCATGAAGGGCCGTCTGTTTGTTGAATTCAACGTGGTGTTTCCCGAGCC

Basic information

species Zea mays
transcript GRMZM2G118731_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 7
gtaggatatatttttttctctttttttgcttgctatatccctttgagctcaactatcctatccaataaaatctcagttctgcatgcactgatattatgttttgttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTTTCATGAAGGGCCGTCTGTTTGTTGAATTCAACGTGGTGTTTCCCGAGCC
           | |  | || | |||||  |  | || || ||         || ||       |||   |||      || |     |||||  ||| |||  | | |||||||||||||||||||| || |||||||| ||||| ||||||||||| ||||||||||| || ||||| ||||||||||||||||||| |||||| |||||
----------gtatgctttcctcttttgactcttttacccatt--------gctgtctgcctttatagtttcttg---ttggacatgttgatag-atgattttcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTTTCATGAAAGGTCGTCTTTTTGTTGAATTCAACGTGGAGTTTCCTGAGCC
















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|32928021|gb|CF032833.1|CF032833
EST:     TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAG                         GTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
genomic: TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
EST: gi|110219395|gb|EC901293.1|EC901293
EST:     TGGGCGACAGCTTCTGATCAAATTTGACCCCGGGGAGGTTATTAAACCAG                         GTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
genomic: TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
EST: gi|76293181|gb|DV032749.1|DV032749
EST:     TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAG                         GTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
genomic: TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
EST: gi|76909046|gb|DV163195.1|DV163195
EST:     TTATTAAACCAG                         GTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
genomic: TTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
EST: gi|6095397|gb|AW120064.1|AW120064
EST:     TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAG                         GTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
genomic: TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
EST: gi|60394649|gb|DN227519.1|DN227519
EST:     TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAG                         GTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
genomic: TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
EST: gi|32944392|gb|CF049211.1|CF049211
EST:     TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAG                         GTCAACACAAGGCCATTAGCGATGAAGGTATGCCTCAGCATGGCCGTCCTT
genomic: TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
EST: gi|32927961|gb|CF032773.1|CF032773
EST:     TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAG                         GTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
genomic: TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
EST: gi|24763119|gb|CA398302.1|CA398302
EST:     TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAG                         GTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
genomic: TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
EST: gi|67025522|gb|CO454271.1|CO454271
EST:     TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAG                         GTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
genomic: TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
EST: gi|40302791|gb|CK347178.1|CK347178
EST:     TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAG                         GTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
genomic: TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
EST: gi|78023076|gb|DV491463.1|DV491463
EST:     TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAG                         GTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
genomic: TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
EST: gi|32942851|gb|CF047670.1|CF047670
EST:     TGGGCTACTGTTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAG                         GTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT
genomic: TGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTT

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: 342

TCTCTCACCGAAGCATTGTGTGGCTTCCAGTTTGTTCTTACTCATCTTGATGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTTTCATGAAGGGCCGTCTGTTTGTTGAATTCAACGTGGTGTTTCCCGAGCC


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

TCTCTCACCGAAGCATTGTGTGGCTTCCAGTTTGTTCTTACTCATCTTGATGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTTTCATGAAGGGCCGTCTGTTTGTTGAATTCAACGTGGTGTTTCCCGAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 425

TCTCTCACCGAAGCATTGTGTGGCTTCCAGTTTGTTCTTACTCATCTTGATGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTTTCATGAAGGGCCGTCTGTTTGTTGAATTCAACGTGGTGTTTCCCGAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 358

TCTCTCACCGAAGCATTGTGTGGCTTCCAGTTTGTTCTTACTCATCTTGATGGGCGACAGCTTCTGATCAAATCTGACCCCGGGGAGGTTATTAAACCAGgtaggatata ... gttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTTTCATGAAGGGCCGTCTGTTTGTTGAATTCAACGTGGTGTTTCCCGAGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatccaataaaatctcagttctgcatgcactgatattatgttttgttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTTTCATGAAGGGCCGTCTGTTTGTTGAATTCAACGTGGTGTTTCCCGAGCC
                            cactgat  putative branch site (score: 358)
                                         ttttgtt  putative PPT
                                 atattatgttttgtt  TA-rich tract