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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttcctatgtgccattgtcgttcatatgatctccctgatttatatgccagtgtggttcatattatctttgatccctctagcttgttaataatgtttgtgtataatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATTAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTAC

Basic information

species Zea mays
transcript GRMZM2G081653_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 2
gtaggttcctatgtgccattgtcgttcatatgatctccctgatttatatgccagtgtggttcatattatctttgatccctctagcttgttaataatgtttgtgtataatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATTAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTAC
                                || || | || |  ||||  |   | |||| |   || |||||| | | ||      |||| |   || | | |    |||||||||||||||||||||||||||| |||||||| || ||||||||||||||  |||| |||||||| |||||||||||||||||||| |||||||||||||
------------------------------gtatgtcacagagtcttatggtataatagttcttccaatatttgattcatgtactactctaattaatattatttgttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATCCGGGGTGCTTTAAGGGCTGAAAAGCCAGAGTTGCTCACTGTAATTTTAC

upper sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 3
-------------------------------gtaggttcctatgtgccattgtcgttcatatgatctccctgatttatatgccagtgtggttcatattatctttga---tccctctagct---tgttaataatgtttgtgtata-atttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATTAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTAC
                                || | |    |||    |||| |  || |  || |     |||  |    |||| | |||   ||| |  || |   | ||  |||||   | | |  | |  ||||  ||   |||| ||||||||||||||| ||||||||| || ||||| || ||||| ||||||||  | || |||||||| || || || || |||||||||||||| || ||||
gtaagtttctgttattttactctatagtatcatatgctttcttgtagtcttgtggaacacaatatatggtgaattggtgatgcagtatagttatgatttttgttaacaattccaatagctgtgtctcacaacttcttgtccatctgtttgtagAAAAATCATATATACACATCTGGAGCATCTGGGACTAATGCTGCTGTTATCCGAGGTGCTTTAAGGGCAGAGAAACCGGAGTTGCTTACTGTTATATTAC

upper sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G00330.1 (Glycine max), 3'ss of exon 3
---------------------------------gtaggttcctatgtgcca---ttgtcgttcatatgatctccctgatttatatgccagtgtggttcat-attatctttgatccctcta------gcttgttaataatgtttgtgtata-atttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATTAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTAC
                                  | | ||     ||  ||   |||| |  || |  || |     |||  |    ||||     | || ||| |  || |   ||| |      |  | | |  | |  ||||  ||   |||| |||||||||||||||  |||||||| || ||||| || ||||| ||||||||| | || |||||||| || || || |||||||||||||| || || ||||
gtaagttgttattttactcaagagtattatatgcttgcttgaagagtttcagtcttgtagaacacaatatatggtgaattggtgatgcagtactagttatgatttttgttaacaactccaatggctgtgtctcacaacttcttgtccatctgtttgtagAAAAATCATATATATACATCTGGAGCATCTGGGACTAATGCTGCTGTTATTCGAGGTGCTTTAAGGGCAGAGAAACCAGAGTTGCTTACAGTTATATTAC

upper sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaggttcctatgtgccattgtcgttcatatgatctccctgatttatatgccagtgtggttcatattatctttgatccctctagcttgttaataatgtttgtgtataatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATTAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTAC
                              | |       ||  |  || |   |||| || |      ||  ||||| | ||     |   |    |   |   |   ||||||||||||||||||| |||||| || || |||||||| ||||| || || || || || || || ||||| || |  |||||| ||||||| |||||| |||
-----------------------------gtaagtcattagaacttcatcctcttgtgtttga------ctccgatccatttaaaacatctctcgaataattcggtttcttgcagAAAAATCATATATACACATCAGGTGCATCTGGAACTAATGCTGCAGTCATCAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTAC

upper sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 4
gtaggttcctatgtgccattgtcgttcatatgatctccctgatt-tatatgccagtgtggttca-tattatctttgatccctctagcttgttaataatgtttgtg-------tataatt------tgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATTAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTAC
||| | | || |      |    ||  || | || ||    ||| |   |||   |   |  ||  ||  |  | |  | ||| |  ||  || | ||| || ||       ||| |||      | |||||||| || || || ||||| || || ||||| || |||||||||||||| || || ||  ||||||| || || |||||| ||||||||||||| ||||
gtatgatgctgtaacttctatcagtatattttatgtctaacattgtgggtgcttattgagcccaacatgctgctgggactctccattttcatattcatgcttctgaaattcctatgattatttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATCAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTAC

upper sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S134_28V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaggttcctatg-tgccattgt-cgttcatatgatctccctgatttatatgccagtgtggttcat-attatctttgatccctctagcttgttaataatgtttgtgtataatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATTAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTAC
           || || || ||| | || ||  |  ||||   | | || | |||   |  | ||| |||    |  ||    ||    |  |  | || ||| |||     ||| |||| ||||||||||  |||||||| ||  | ||||||||||| || ||||| ||||| || || ||||||||||  |||||  | |||||||||||| | |
-----------tgctgtcagtgtaccttaatcagtactccaaaagtaattttccacaat--tccatcattgcagtgcatagaactcaactccttttcatttttctgt-----ttgtagAATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATAAGGGGAGCATTGAGAGCTGAAAGACCAGACCTTCTTACTGTAATTCTGC

upper sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S323_60V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaggttcctatgtgccattgtcgttcatatgatctccctgatttatatgccagtgtggttcatattatctttgatccctctagcttgttaataatgtttgtgtataatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATTAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTAC
 || |   |   || | | |||| |  ||||  |   |    |||                    | | |||   |    ||||    |   |||   || | |    |||  |||||||||| || |  ||||| || ||  | |||||||| ||||||||||| ||||| || || ||||||||||  |||||  | |||||||||||| |||
atacgaatcagagttctactgtcatg-atatcgtaatcacagttt---------cacaaccttcttcaacttcagtg---ctagaccatatttaactcttctcttcgtttt--agAAAAATCACATTTATACATCAGGAGCAGCGGGAACAAACGCAGCTGTTATAAGGGGAGCATTGAGAGCTGAAAGACCAGACCTCCTTACTGTAATTCTAC

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|50329846|gb|CO524972.1|CO524972
EST:     TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACA                         AAAAATCATATATTCACATCTGGGGCTTCTG
genomic: TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACAgtaggttcct ... taatttgcagAAAAATCATATATTCACATCTGGGGCTTCTG
EST: gi|89764107|gb|DY691035.1|DY691035
EST:     TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACA                         AAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
genomic: TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACAgtaggttcct ... taatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
EST: gi|78075488|gb|DV503922.1|DV503922
EST:     TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACA                         AAAAATCATATATTCACATCTGGNGCTTCTGGAACAAATGCAGCTGTTATT
genomic: TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACAgtaggttcct ... taatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
EST: gi|31363700|gb|CD448057.1|CD448057
EST:     TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACA                         AAAAATCATATATTCACATTTGGGGC
genomic: TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACAgtaggttcct ... taatttgcagAAAAATCATATATTCACATCTGGGGC
EST: gi|74241321|gb|DT649235.1|DT649235
EST:     TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACA                         AAAAATCATATATTCACATCTGGGGGCTTCTGGAACAAATGCAGCTGTTAT
genomic: TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACAgtaggttcct ... taatttgcagAAAAATCATATATTCACATCTGGGG-CTTCTGGAACAAATGCAGCTGTTAT
EST: gi|71445741|gb|DR826791.1|DR826791
EST:     TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACA                         AAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
genomic: TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACAgtaggttcct ... taatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
EST: gi|32798841|gb|CD951077.1|CD951077
EST:     GATCCTGAGCTATGCTATGGTCATAACA                         AAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
genomic: GATCCTGAGCTATGCTATGGTCATAACAgtaggttcct ... taatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
EST: gi|149090139|gb|EE179439.2|EE179439
EST:     TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACA                         AAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
genomic: TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACAgtaggttcct ... taatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
EST: gi|76911678|gb|DV164374.1|DV164374
EST:     TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACA                         AAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
genomic: TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACAgtaggttcct ... taatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
EST: gi|148973267|gb|EE024347.2|EE024347
EST:     TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACA                         AAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
genomic: TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACAgtaggttcct ... taatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
EST: gi|149014320|gb|EE043899.2|EE043899
EST:     TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACA                         AAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
genomic: TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACAgtaggttcct ... taatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
EST: gi|71421265|gb|DR805363.1|DR805363
EST:     TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACA                         AAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT
genomic: TTATGCACCAACAGCTTATTGAGATCCTGAGCTATGCTATGGTCATAACAgtaggttcct ... taatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatattatctttgatccctctagcttgttaataatgtttgtgtataatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATTAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTAC
                          tgttaat  putative branch site (score: 3)
                            ttaataatgtttgtgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggttcctatgtgccattgtcgttcatatgatctccctgatttatatgccagtgtggttcatattatctttgatccctctagcttgttaataatgtttgtgtataatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATTAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA