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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttctttcactgcagtttggaatttttttgtatcaatcaagtgtaaaacattgcggtcatttctttacatacctgacgttgctgtataactcaatagattccctttccccctagtcccctaccactatgattcttaaaaatatgtcccttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT

Basic information

species Zea mays
transcript GRMZM2G315931_T02
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G315931_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os08g37950.1 (Oryza sativa), 3'ss of exon 15
gtaatttctttcactgcagtttggaatttttttgtatcaatcaagtgtaaaacattgcggtcatttctttacatacctgacgttgctgtataactcaatagattccctttccccctagtcccct---accactatgattcttaaaaata--------tgtcccttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT
||||| || |   |  || |||| |||||     |     | |||  | ||| ||      || |  |||  || | ||   ||||||    |||||||  | |     |     ||  ||  |   | | ||    ||| | |||| |        | | | |   ||||||||| | ||||||||||||||||||||||||||||||| ||| |||||||||||||||||||||||||| ||||| ||||||
gtaatctcatatgcaacaatttgaaatttgcgaattc---ttaagcatgaaaaatc-----cactgttttgtattcttggtattgctgccagactcaattaacttttactttttgtatgccgatttaatctcttcttttcctgaaaaaaaattcgagtcttcttgtcatgcagCTTGTTGATGCTTTAGAGTTGAGTAAAGAGACCATGAGGACAGTGAAGCAAAATCTTTGGTGGGCTTTTCTGTACAACATT

upper sequence: GRMZM2G315931_T02 (Zea mays), 3'ss of exon 15
lower sequence: AT4G33520.3 (Arabidopsis thaliana), 3'ss of exon 15
gtaatttctttcactgcagtttggaatttttttgtatcaatcaagtgtaaaacattgcggtcatttctttacatacctgacgttgctgtataactcaatagattccctttccccctagtcccctaccac-tatgattcttaaaaatatgtcccttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT----
                                                   | | |||    ||||  ||||  |    | | |  |  ||         | ||||||||  |  |  |    |   ||  ||||   |   |  ||  |   ||| |||||| |  | |||||  | ||| | |||    | ||||||||||| ||||||||||| ||||||||||| |||   || ||||||    
--------------------------------------------------gaaactgc----attttcttactaaatcaatgataatagat---------gtttccctttggctttcatgaatttggacacatgaacttagtagttacatgatttccatgcagTTGCTTGATGCGATGGAGCTAAGTCGGCAAACCATGAAGACCGTGAAGCAAAACCTTTGGTGGGCGTTCGGATACAACATTGTAA

upper sequence: GRMZM2G315931_T02 (Zea mays), 3'ss of exon 15
lower sequence: AT4G33520.2 (Arabidopsis thaliana), 3'ss of exon 15
gtaatttctttcactgcagtttggaatttttttgtatcaatcaagtgtaaaacattgcggtcatttctttacatacctgacgttgctgtataactcaatagattccctttccccctagtcccctaccac-tatgattcttaaaaatatgtcccttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT
                                                   | | |||    ||||  ||||  |    | | |  |  ||         | ||||||||  |  |  |    |   ||  ||||   |   |  ||  |   ||| |||||| |  | |||||  | ||| | |||    | ||||||||||| ||||||||||| ||||||||||| |||   || ||||||
--------------------------------------------------gaaactgc----attttcttactaaatcaatgataatagat---------gtttccctttggctttcatgaatttggacacatgaacttagtagttacatgatttccatgcagTTGCTTGATGCGATGGAGCTAAGTCGGCAAACCATGAAGACCGTGAAGCAAAACCTTTGGTGGGCGTTCGGATACAACATT

upper sequence: GRMZM2G315931_T02 (Zea mays), 3'ss of exon 15
lower sequence: Vv12s0142g00330.t01 (Vitis vinifera), 3'ss of exon 7
gtaatttctttcactgcagtttggaatttttttgtatcaatcaagtgtaaaacattgcggtcatttctttacatacctgacgttgctgtataactcaatagattccctttccccctagtcccctacca--ctatgattcttaaaaatatgtcccttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT
                                                               |  || |   |   ||  | ||||    | |  ||  || |  ||         | ||  |||    ||||||    |  |  |   || | | | ||||| |  | |||||||| ||  | || | |   ||||||||||| ||||| ||||||||||||||||| ||    |||||||||
---------------------------------------------------------------tacctctggtttgatgtggatgcttctcatcctaaatgagtttctggatttagggccctatactgtgctatgaaaaattgacctggatctccttg-tgcagTTGCTTGATGCTTTCGAACTAAGCAGACTAACCATGAAGACCGTGAAACAAAATCTTTGGTGGGCCTTTGCATATAACATT

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|211170369|gb|FL103278.1|FL103278
EST:     CAGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACAGGTTATCCCAG                         CTTCTCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
genomic: CAGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACAGGTTATCCCAGgtaatttctt ... ttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
EST: gi|33094915|gb|CF054909.1|CF054909
EST:     ACTTATGGGCAACAGGTTATCCCAG                         CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
genomic: ACTTATGGGCAACAGGTTATCCCAGgtaatttctt ... ttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
EST: gi|78104271|gb|DV522689.1|DV522689
EST:     CAGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACAGGTTATCCCAG                         CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
genomic: CAGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACAGGTTATCCCAGgtaatttctt ... ttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
EST: gi|13249696|gb|BG360601.1|BG360601
EST:     CAGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACAGGTTATCCCAG                         CTTATCGATGCTTTAGAGTTGAGTAAAGAGTCCATGAAGACGGTGAAGCAA
genomic: CAGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACAGGTTATCCCAGgtaatttctt ... ttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
EST: gi|12968157|gb|BG265104.1|BG265104
EST:     CAGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACAGGTTATCCCAG                         CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
genomic: CAGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACAGGTTATCCCAGgtaatttctt ... ttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
EST: gi|12968156|gb|BG265103.1|BG265103
EST:     AGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACCAGGTTATCCCAG                         CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
genomic: AGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAA-CAGGTTATCCCAGgtaatttctt ... ttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
EST: gi|211170365|gb|FL103274.1|FL103274
EST:     CAGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACAGGTTATCCCAG                         CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
genomic: CAGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACAGGTTATCCCAGgtaatttctt ... ttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
EST: gi|60397501|gb|DN230317.1|DN230317
EST:     CAGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACAGGTTATCCCAG                         CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
genomic: CAGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACAGGTTATCCCAGgtaatttctt ... ttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
EST: gi|211170368|gb|FL103277.1|FL103277
EST:     CAGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACAGGTTATCCCAG                         CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA
genomic: CAGCTAGTGATGTATCTTCAGTTGTACTTATGGGCAACAGGTTATCCCAGgtaatttctt ... ttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccccctagtcccctaccactatgattcttaaaaatatgtcccttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT
                                       tgtcccttc  CT-rich tract
                      tatgattcttaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttctttcactgcagtttggaatttttttgtatcaatcaagtgtaaaacattgcggtcatttctttacatacctgacgttgctgtataactcaatagattccctttccccctagtcccctaccactatgattcttaaaaatatgtcccttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG