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

gtaaattatttttttggctcttgatggcagtgtaggatagccaccgtgctttttcttgctgatggattaacaataaccgaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGCATCGCCGAGAAGTTGAACACTGCTGCTCAGGCGCTGTGACTTTGGTTGT

Basic information

species Zea mays
transcript GRMZM2G098153_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098153_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g01450.1 (Oryza sativa), 3'ss of exon 5
gtaaattatttttttggctcttg---atggcagtgtaggatagccaccgtgctttttcttgctgatggat-taacaataaccgaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGCATCGCCGAGAAGTTGAACACTGCTGCTCAGGCGCTGTGACTTTGGTTGT-
     ||| |  ||| |||  |    |||  |||  | ||    ||   |   ||||||||   ||     |  ||  |   |      |||||||| ||||| ||||| |||||||||||||||||||||||||| || ||||| ||||||||||||||||| || || ||    |||| | ||   | || 
----gttagtgctttagcttgtcggtatgcgagtaaatgaatatcattttcaattttcttgtacataatcattgcaccatttggtgatgcagGATAATCTTGCACTGGTGTACCTGTCAAGCATCACAAGGACACAGATTAGCATAGCCGAGAAGTTGAACACCGCCGCCCAAATCCTGTAATTTCCAT-GTA

upper sequence: GRMZM2G098153_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 5
------------gtaaattatttttttggctcttgatggcagtgtaggatagccaccgtgctttttcttgctgatg-gattaacaataaccgacccc-acagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGCATCGCCGAGAAGTTGAACACTGCTGCTCAGGCGCTGTGACTTTGGTTGT
            ||  ||| || | || | || |  ||  |    |  ||   ||  ||   | |    |   |   ||||  |  |  | |        ||||  || |    ||  | ||| ||||||||||||||||||||||  | ||| | || || ||||||||||| ||||||||    | || ||     |   
tctgttgcttctgtccattgttgtgtttgatcat--tgaaaacccacaatttgcatggtttatctcaccgtaaaaatgattttcttttcctgttttttgtagGACCACTTACTCCTACTGTACTTGTCAAGCATCACAAGGACACAGCTGAGCTTAGCGGAAAAGTTGAACACAGCTGCTCAAATCCCGTAACCCATATCCA
















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|60394964|gb|DN227833.1|DN227833
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|71439970|gb|DR821020.1|DR821020
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|67015095|gb|CO443844.1|CO443844
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|149112626|gb|EE295475.2|EE295475
EST:     GAAA-TGTCCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: GAAATTGT-CCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|71439969|gb|DR821019.1|DR821019
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|16919791|gb|BM074356.1|BM074356
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|37399477|gb|CF637068.1|CF637068
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|76286914|gb|DV026482.1|DV026482
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|15499459|gb|BI595972.1|BI595972
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|60358158|gb|DN225131.1|DN225131
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|93015003|gb|EB640523.1|EB640523
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|6526821|gb|AW216090.1|AW216090
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|19822328|gb|BQ048352.1|BQ048352
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|6057055|gb|AW091460.1|AW091460
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|78091175|gb|DV519549.1|DV519549
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|101382033|gb|EB813072.1|EB813072
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|93015004|gb|EB640524.1|EB640524
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTG
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTG
EST: gi|76284328|gb|DV023896.1|DV023896
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|83278726|gb|DV942734.1|DV942734
EST:     CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAG                         GATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: CGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC
EST: gi|67011620|gb|CO440369.1|CO440369
EST:     GAAATTGTCCCCAGCTGCTTTCGATAAAGCTTT-CAATGACAAGATTCAG                         GATAACCTTGCGCTGGTTTACCTGTCAAGCATCACAAGGACACAAATCAGC
genomic: GAAATTGTCCCCAGCTGCTTTCGATAA-GCTTTTCAATGACAAGATTCAGgtaaattatt ... gaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggatagccaccgtgctttttcttgctgatggattaacaataaccgaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGCATCGCCGAGAAGTTGAACACTGCTGCTCAGGCGCTGTGACTTTGGTTGT
                                     caataac  putative branch site (score: 2)
                                attaacaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattatttttttggctcttgatggcagtgtaggatagccaccgtgctttttcttgctgatggattaacaataaccgaccccacagGATAACCTTGCGCTGGTATACCTGTCAAGCATCACAAGGACACAAATCAGCATCGCCGAGAAGTTGAACACTGCTGCTCAGGCGCTGTGACTTTGGTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT