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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcatttcctctatccttccaataatagatgtcttgtattatcattctattctagtgtttccttggattttaattttccatctgtcatcttttcaagcagTGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGTTCAGCGTAGGGGGAAATTACAGGACCTGCACCGCTCAGTGCAAGAAATA

Basic information

species Zea mays
transcript GRMZM2G101053_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101053_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g42970.2 (Oryza sativa), 3'ss of exon 3
------gtgcatttcctctatccttccaataatagatgtcttgtattatcattctattctagtgtttccttggattttaattttccatctgtcatcttttcaagcagTGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGTTCAGCGTAGGGGGAAATTACAGGACCTGCACCGCTCAGTGCAAGAAATA
       || || |   | ||   |||||  |||| |  ||||||    ||  |  || |||  |     | |||| |  |||||  | | |  || ||  || ||||||  |||||||||| ||||||||||||||||||||| || ||||  |||| ||| | || ||  || | || || ||| |    || ||||||||||| 
gttaaaatggatatttgccat---tccaagtatagtt--cttgtacg--cagccgcttgtagcatccttattgattctg-ttttctgtttattgtcctta-aaacagTGCATTAGCTAGTCTCCCTGACAGCTTGAAAGAAAAATTGTTGCCCAATGTCCAGTGCAGAGGACAACTCCAAGAACTGAATAATTCTGTGCAAGAAATT
















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|60346950|gb|DN213923.1|DN213923
EST:     CAATCTGTAAACGTTGGCTACAAATGGGGCCTTGTTCGTGGGGTTGGCAG                         TGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGT
genomic: CAATCTGTAAACGTTGGCTACAAATGGGGCCTTGTTCGTGGGGTTGGCAGgtgcatttcc ... tttcaagcagTGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGT
EST: gi|74242636|gb|DT650550.1|DT650550
EST:     CAATCTGTAAACGTTGGCTACAAATGGGGCCTTGTTCGTGGGGTTGGCAG                         TGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGT
genomic: CAATCTGTAAACGTTGGCTACAAATGGGGCCTTGTTCGTGGGGTTGGCAGgtgcatttcc ... tttcaagcagTGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGT
EST: gi|89760622|gb|DY688955.1|DY688955
EST:     CAATCTGTAAACGTTGGCTACAAATGGGGCCTTGTTCGTGGGGTTGGCAG                         TGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGT
genomic: CAATCTGTAAACGTTGGCTACAAATGGGGCCTTGTTCGTGGGGTTGGCAGgtgcatttcc ... tttcaagcagTGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGT
EST: gi|93282479|gb|EB674743.1|EB674743
EST:     CAATCTGTAAACGTTGGCTACAAATGGGGCCTTGTTCGTGGGGTTGGCAG                         TGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGT
genomic: CAATCTGTAAACGTTGGCTACAAATGGGGCCTTGTTCGTGGGGTTGGCAGgtgcatttcc ... tttcaagcagTGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGT
EST: gi|60339381|gb|DN206354.1|DN206354
EST:     AATGGGGCCTTGTTCGTGGGGTTGGCAG                         TGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGT
genomic: AATGGGGCCTTGTTCGTGGGGTTGGCAGgtgcatttcc ... tttcaagcagTGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGT
EST: gi|71307868|gb|DR790155.1|DR790155
EST:     CAATCTGTAAACGTTGGCTACAAATGGGGCCTTGTTCGTGGGGTTGGCAG                         TGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGT
genomic: CAATCTGTAAACGTTGGCTACAAATGGGGCCTTGTTCGTGGGGTTGGCAGgtgcatttcc ... tttcaagcagTGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGT
EST: gi|149064879|gb|EE286550.2|EE286550
EST:     CAATCTGTAAACGTTGGCTACAAATGGGGCCTTGTTCGTGGGGTTGGCAG                         TGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGT
genomic: CAATCTGTAAACGTTGGCTACAAATGGGGCCTTGTTCGTGGGGTTGGCAGgtgcatttcc ... tttcaagcagTGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattctagtgtttccttggattttaattttccatctgtcatcttttcaagcagTGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGTTCAGCGTAGGGGGAAATTACAGGACCTGCACCGCTCAGTGCAAGAAATA
                      ttttaat  putative branch site (score: 3)
                            ttttccatctgtcatc  CT-rich tract
                 ttggattttaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcatttcctctatccttccaataatagatgtcttgtattatcattctattctagtgtttccttggattttaattttccatctgtcatcttttcaagcagTGCGCTAGCTAGTCTTCCTGACAGCTTGAAAGAAAAACTGGTGCCGGATGTTCAGCGTAGGGGGAAATTACAGGACCTGCACCGCTCAGTGCAAGAAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA