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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgccttctaccttctctttgcacagtttctaagtaattctgccggctaattttgtttggttatttaattatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTTACCATGGAGTGGCTGGAGAACTACTGCAAGAACAAGGCTGCCTGAAGCT

Basic information

species Zea mays
transcript GRMZM2G063909_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 19
--------------------------------------gtctgccttctaccttctctt----tgcacagt-ttctaagtaattctgccggctaattttgtttggttatttaattatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTTACCATGGAGTGGCTGGAGAACTACTGCAAGAACAAGGCTGCCTGAAGCT
                                       ||| |  |  |  || |  |    |||| ||  | ||   | |||||  |  | |||| | |    |||| |     ||  ||||||||| ||||||||||| ||||||||||| ||||| || || ||||| || ||||||||||||||||||||| ||||||||||    ||||| |||||||
gtatctctcactttccactttctacctcatttctttggatcttctctgcattttgtactacaatgcagaggatccttcttcattctatcaaccaattctttcacattatctg----tgtcgcagCTCATTTGGGACCGTGCTCTTGGCCTGCCGCTCGAAAGACCGAAGAGTGTCACCATGGAGTGGCTGGAGAACCACTGCAAGAAGGTTGCTGCTTGAAGCT

upper sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 19
gtctgccttctaccttc---tctttgcacagtttctaagtaattctgccggctaattttgtttggttatttaat-tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTTACCATGGAGTGGCTGGAGAACTACTGCAAGAACAAGGCTGCCTGAAGCT
|| |   |  | |||||   | | | |    ||  | ||   || |  |  | |||| ||  | || ||  | | | |    |||||||| ||||||||||| ||||| ||||| ||||| || || ||||| || ||||||||||||||||| ||| ||||||||||    ||||| |||||||
gtatatttcttcccttcaactgtctacctctttcttcagatcttgtatcaaccaattctgacttgtgatacattatgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTCACCATGGAGTGGCTGGAAAACCACTGCAAGAAGGCTGCTGCTTGAAGCT

upper sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 18
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 19
------------------------gtctgccttctaccttctc----tttgcacagtttctaag-----taattctgccggctaattttgtttggttatt-taattatgatg--------cagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTTACCATGGAGTGGCTGGAGAACTACTGCAAGAACAAGGCTGCCTGAAGCT
                         | |  ||||| ||||  |    ||||     ||||| |      | ||||| ||  |   |     |   | ||| | ||||| ||         ||| | || ||||||||||| |||||  |||| || |||||||| || || ||||| ||||| ||||| || ||| ||||||||||    || |||| |  ||
gttctcactatgtccctcaccttcttttctcttctccctttccgtattttgtttgttttcttaaatctctcattcttccttcgggtgcatctgaatcattattattattatttcttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTTACAATGGAATGGCTTGAAAACCACTGCAAGAAAGCAGCCGCCTAATTCT

upper sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 18
lower sequence: EFJ25084 (Selaginella moellendorffii), 3'ss of exon 18
gtctgccttctaccttctctttgcacagtttctaagtaattctgccggctaattttgtttggttatttaattatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTTACCATGGAGTGGCTGGAGAACTACTGCAAGAACAAGGCTGCCTGAAGCT
                           ||       |  | || ||       |    |||  |  ||   |||  | |||||  | ||||| || || ||||| || ||| | || ||||| |||||| | ||||||||||||||||||||||| ||||||||  |  | |    |   |
---------------------------gtactagcattgtgcttccaagct-ctccaattgactgcttg--tatccttcagCTGGTGTGGGATCGCGCACTTGGTCTTCCAATTGAAAGGCCAAAGAGCATGACCATGGAGTGGCTGGAGAACTATTGCAAGAAGCAAACCGTGACAGCGT

upper sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 18
lower sequence: EFJ29959 (Selaginella moellendorffii), 3'ss of exon 18
gtctgccttctaccttctctttgcacagtttctaagtaattctgccggctaattttgtttggttatttaattatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTTACCATGGAGTGGCTGGAGAACTACTGCAAGAACAAGGCTGCCTGAAGCT
               |  | |||    | ||| |||   | |    | ||    |||| | ||   ||          |||||  | ||||| || || ||||| || ||| | || ||||| |||||| | ||||||| ||||||||||||||| ||||||||  |  | |    |   |
-----------gtactaccattgt---gcttccaagctctccaattgactg--cttgtatcgtacctt----------cagCTGGTGTGGGATCGCGCACTTGGTCTTCCAATTGAAAGGCCAAAGAGCATGACCATGGGGTGGCTGGAGAACTATTGCAAGAAGCAAACCGTGACAGCGT

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|211314255|gb|FK994155.1|FK994155
EST:     ATCACACTGTCTTGTTCGGTGTTTCGAGAANCATGGGGGTAGGATCCCAG                         CTCATCTGGGACCGTGCCCCTTGGCCTGCCACTCGAGAG
genomic: ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAGgtctgccttc ... tatgatgcagCTCATCTGGGACCGTGCCC-TTGGCCTGCCACTCGAGAG
EST: gi|14208440|gb|BG842118.1|BG842118
EST:     ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTT
genomic: ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAGgtctgccttc ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTT
EST: gi|60357508|gb|DN224481.1|DN224481
EST:     ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTT
genomic: ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAGgtctgccttc ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTT
EST: gi|78076903|gb|DV505337.1|DV505337
EST:     ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTT
genomic: ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAGgtctgccttc ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTT
EST: gi|60345083|gb|DN212056.1|DN212056
EST:     ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCA
genomic: ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAGgtctgccttc ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCA
EST: gi|50331232|gb|CO526358.1|CO526358
EST:     ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTT
genomic: ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAGgtctgccttc ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTT
EST: gi|40334210|gb|CK368280.1|CK368280
EST:     ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTC
genomic: ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAGgtctgccttc ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTC
EST: gi|60400601|gb|DN233408.1|DN233408
EST:     ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTT
genomic: ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAGgtctgccttc ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTT
EST: gi|60354991|gb|DN221964.1|DN221964
EST:     ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCA
genomic: ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAGgtctgccttc ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCA
EST: gi|17932431|gb|BM269391.1|BM269391
EST:     ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTT
genomic: ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAGgtctgccttc ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTT
EST: gi|37394364|gb|CF634455.1|CF634455
EST:     ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTT
genomic: ATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAGgtctgccttc ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttctaagtaattctgccggctaattttgtttggttatttaattatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTTACCATGGAGTGGCTGGAGAACTACTGCAAGAACAAGGCTGCCTGAAGCT
                       taattttgtttggtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgccttctaccttctctttgcacagtttctaagtaattctgccggctaattttgtttggttatttaattatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTTACCATGGAGTGGCTGGAGAACTACTGCAAGAACAAGGCTGCCTGAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC