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

gtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacgctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT

Basic information

species Zea mays
transcript GRMZM2G026470_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 3'ss of exon 5
gtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacgctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT
                            |    ||||| | | | ||||    | || |  |    |   |||| | |    | | | |   |||||            ||||||| || | || ||     |  || ||||||||||||| |||||||||||||| || ||||| |||||| |||| ||  |  | || || ||||| ||||||||||| ||
---------------------------gtacgcctgcttcctca-gctcatacgattgctacattttttatgcttggtattgcac-cttgatttcaa------------ttgttttatt-cttgatcaaa--atctttcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCTTGCCTGCTCCGACAGCTCGTGAAGCAATCCAGTACTCTAT

upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacg-ctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT
                                                 |  || |            ||||    |||  |   ||     |   |||| |    |      || |   ||  | |  |      || |||| |||||||||||||||||| | ||||| |||||||| ||| ||||  | |    ||| |  ||||| || |||||||||||
-------------------------------------------------gtaagatccttat----ctcttgtcaaatcaaataactaaggaccaaaactaaagaagc-----ttataaatcgcgtttgg------tttcagATAAGAAGAACGAGAACAAGAAAGTGGCTGTCAACGATTTCTTGCCATCAGAGAGTGCACATGAAGCTATTCAGTACTCCAT

upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 4
lower sequence: EDP02064 (Chlamydomonas reinhardtii), 3'ss of exon 3
---------------------gtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcg-ctaggtttccgcgcggt---ccttgctggatcggacgctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagAC---AAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT-
                     |   ||    |       | |    |||   |   |     ||| || |  ||  |     | || |    ||  | ||    |  | |  |  ||  | | ||     | || |   |     | ||||   |     |    |||   |||||||||||| |||||||||||| |||  |||||||||||   || |  |  |||    | |   || || ||||  | 
gtgcgtacgtgcgggaaaacagggagcctcagggaaaggtgtg-ggatagtgccaagtcggatgaggcgcaactcagcagtagagcagcaagccgagatgtgctgaccacgtccaccaacgagtgctgacgcggcttcgtctgaccgtgctgcagGTTCTTCGAGGACTACAAGAAGAACGAGCACAAGGAGGTGGTCGTGGACGACTTCCTGGGTGCTGAGGAGGCCAAGAAGGTGGTCAAGGACTCGCTG

upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ33440 (Selaginella moellendorffii), 3'ss of exon 6
gtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacgctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT
                                                      || |||     || |  ||||  |  |      |    |  || |  |  | |  |||| |  |||| |   ||||    | || ||||||||||||||||||||||   ||||| || |||||||||||||| || |     |||    | || |||||| | |||||
------------------------------------------------------gtatcc-ttttgtgccggctgtgtgag------cgtgttggaattttctctct--ttgtctgctttctttaactggagggagtc-agACAAGAAGAACGAGAACAAGACCGTGGCTGTGAACGACTTCCTGCCAGCAGAAAACGCCGTGCAGGCGATCCAGCATTCCAT

upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ27219 (Selaginella moellendorffii), 3'ss of exon 6
gtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacgctcctccct-tcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT
                                                              |    | ||  ||   |||  |      | | |          | |  |||| |  |||| |   ||||    | || ||||||||||||||||||||||   ||||| || |||||||||||||| || |     |||    | || |||||| | |||||
--------------------------------------------------------------gtatccttttgtgtgccggctgtgtgagcgtgttggaattttctctctttgtctgctttctttaactggagggagtc-agACAAGAAGAACGAGAACAAGACCGTGGCGGTGAACGACTTCCTGCCAGCAGAAAACGCCGTGCAGGCGATCCAGCATTCCAT

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|32831350|gb|CD971028.1|CD971028
EST:     TGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT
EST: gi|33098670|gb|CF058630.1|CF058630
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT
EST: gi|78023075|gb|DV491462.1|DV491462
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTGGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAATGACTTCTTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|28984521|gb|BQ539133.2|BQ539133
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|71331880|gb|DR802818.1|DR802818
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|62550248|gb|DN830668.1|DN830668
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|78121801|gb|DV540185.1|DV540185
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|5499294|gb|AI855161.1|AI855161
EST:     CGAGCTCTCCCCTCNCCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|60354156|gb|DN221129.1|DN221129
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT
         aactgac  putative branch site (score: 2)
                          ttttgttt  TA-rich tract