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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggttcgggtttggaaaccccagctcttctttctctactcctgtggtctagctattgttgatgcccggatgctctgtcccgagcccgattattgatgttctcttttgaactcgtgcagCGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGACAAGGGGAACTCGGTGCCCAAGATCCTTCTGCTCATGCAAGAGAGGCTG

Basic information

species Zea mays
transcript GRMZM2G143253_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143253_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g22580.1 (Oryza sativa), 3'ss of exon 1
gtcggttcgggtttggaa---accccagctcttctttctctactcctgtggtcta-gctattgttgatgcc--cggatgctctgtcccga-gcccgatt-----attgatgttctcttttgaactcgtgcagCGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGACAAGGGGAACTCGGTGCCCAAGATCCTTCTGCTCATGCAAGAGAGGCTG
||| || |  || |       |  || || || |        ||   |   |||| ||      |||| ||  ||| |  | | || ||  |   ||||      || ||||||| | ||||   ||||||| || ||||| ||||| || ||||| ||||||||||||||  ||| ||| ||||| |||||||||||||||||||| ||  | |||||||| |||||||||
gtcagtactagtatacgttgtatgcctgccctgccgcgcgcgctggcgaaatctaagcctgcaatgattcctccggttaatgtctctcggcgttggatttaccggttaatgttct-tcttgattccgtgcagTGCGAGCGTTTTCGGCGTGTCACCTGAGTCGATGCAGTGCTGCTTCGACGACAACGGGAACTCGGTGCCCAAGATTCTGTTACTCATGCAGGAGAGGCTG
















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|78105267|gb|DV523685.1|DV523685
EST:     CTCCCCGTCGAGTTCGAGCTCGAGATCCCCGGCCAGGTCCCCAGCGCCAG                         CGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGA
genomic: CTCCCCGTCGAGTTCGAGCTCGAGATCCCCGGCCAGGTCCCCAGCGCCAGgtcggttcgg ... actcgtgcagCGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGA
EST: gi|71446992|gb|DR828042.1|DR828042
EST:     CTCCCCGTCGAGTTCGAGCTCGAGATCCCCGGCCAGGTCCCCAGCGCCAG                         CGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGA
genomic: CTCCCCGTCGAGTTCGAGCTCGAGATCCCCGGCCAGGTCCCCAGCGCCAGgtcggttcgg ... actcgtgcagCGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGA
EST: gi|76920416|gb|DV168162.1|DV168162
EST:     CTCCCCGTCGAGTTCGAGCTCGAGATCCCCGGCCAGGTCCCCAGCGCCAG                         CGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGA
genomic: CTCCCCGTCGAGTTCGAGCTCGAGATCCCCGGCCAGGTCCCCAGCGCCAGgtcggttcgg ... actcgtgcagCGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGA
EST: gi|94476795|gb|EB705753.1|EB705753
EST:     CTCCCCGTCGAGTTCGAGCTCGAGATCCCCGGCCAGGTCCCCAGCGCCAG                         CGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGA
genomic: CTCCCCGTCGAGTTCGAGCTCGAGATCCCCGGCCAGGTCCCCAGCGCCAGgtcggttcgg ... actcgtgcagCGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGA
EST: gi|76014770|gb|DT941940.1|DT941940
EST:     CTCCCCGTCGAGTTCGAGCTCGAGATCCCCGGCCAGGTCCCCAGCGCCAG                         CGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGA
genomic: CTCCCCGTCGAGTTCGAGCTCGAGATCCCCGGCCAGGTCCCCAGCGCCAGgtcggttcgg ... actcgtgcagCGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGA
EST: gi|50329448|gb|CO524574.1|CO524574
EST:     CTCCCCGTCGAGTTCGAGCTCGAGATCCCCGGCCAGGTCCCCAGCGCCAG                         CGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGA
genomic: CTCCCCGTCGAGTTCGAGCTCGAGATCCCCGGCCAGGTCCCCAGCGCCAGgtcggttcgg ... actcgtgcagCGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccggatgctctgtcccgagcccgattattgatgttctcttttgaactcgtgcagCGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGACAAGGGGAACTCGGTGCCCAAGATCCTTCTGCTCATGCAAGAGAGGCTG
                          tattgat  putative branch site (score: 3)
                        attattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggttcgggtttggaaaccccagctcttctttctctactcctgtggtctagctattgttgatgcccggatgctctgtcccgagcccgattattgatgttctcttttgaactcgtgcagCGCCAGCGTGTTCGGGGTATCACCGGAGTCGATGCAGTGTGGCTACGATGACAAGGGGAACTCGGTGCCCAAGATCCTTCTGCTCATGCAAGAGAGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG