Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggagtacgtactaagaatttcatctaatgaaagcaaattactagctgttgtttagtcgatcagcctgttgcgcactgctgactttgttctctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCCGTTGCTATGCTGGTCTCAATGGGCTTTGATGGCAATAACGCAAGGCAGG

Basic information

species Zea mays
transcript GRMZM2G157316_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157316_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g16330.1 (Oryza sativa), 3'ss of exon 7
gggagtacgtactaagaattt--catctaatgaaagcaaattactagctgttgtttagtcgatcagcctgttgcgcac-tgctgactttgttctctcaa-gcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCCGTTGCTATGCTGGTCTCAATGGGCTTTGATGGCAATAACGCAAGGCAGG
   |  | | || ||   |||  |||||        | ||  | |  |||      |  | || |   | | ||  || |  ||| | |||    | ||   ||||  | |   || ||||||| || ||| |||||||||| ||||| || ||  | ||||||||||| || |||||||||||||| |||   ||||| ||||
---acaaggcacgaaacctttatcatctctgagttcctaagcattgcctgaaagaaaaccaatgactatat-gcttacatcttgattctgtctatttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCAATCGCTATGCTGGTTTCGATGGGCTTTGATGGAAATGCTGCAAGACAGG
















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|45568649|gb|CK986167.1|CK986167
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|28985536|gb|CB350690.1|CB350690
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|93013634|gb|EB639154.1|EB639154
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|18170113|gb|BM339953.1|BM339953
EST:     ACAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|18174318|gb|BM349706.1|BM349706
EST:     CCAGAAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|88748362|gb|DY532503.1|DY532503
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|74232243|gb|DT640157.1|DT640157
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|18162122|gb|BM331961.1|BM331961
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|111192662|gb|EE290798.1|EE290798
EST:     CATAGAGGCCGTGGGGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCCTC
genomic: CATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGT-CCTC
EST: gi|12968576|gb|BG265522.1|BG265522
EST:     CCAGGAGTCTTGTTGGGAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|33091544|gb|CF051538.1|CF051538
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|18165927|gb|BM335766.1|BM335766
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGACCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|93013208|gb|EB638728.1|EB638728
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|71305917|gb|DR789089.1|DR789089
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|71433037|gb|DR814087.1|DR814087
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|86470086|gb|DY236456.1|DY236456
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttgtttagtcgatcagcctgttgcgcactgctgactttgttctctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCCGTTGCTATGCTGGTCTCAATGGGCTTTGATGGCAATAACGCAAGGCAGG
                               tgctgac  putative branch site (score: 2)
                                     ctttgttctctc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggagtacgtactaagaatttcatctaatgaaagcaaattactagctgttgtttagtcgatcagcctgttgcgcactgctgactttgttctctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCCGTTGCTATGCTGGTCTCAATGGGCTTTGATGGCAATAACGCAAGGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG