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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattccttttgtagatgttatactttcagttgttcagtatagccatctagtttttccatatgccatctgtagtaccttacttttggttcatatttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCC

Basic information

species Zea mays
transcript GRMZM2G097226_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097226_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 11
gtaattccttttgtagatgttatactttcagttgttcagt--atagc-catctagtttttc---catatgccatctgtagtaccttacttttggttcatatttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCC
|| ||  ||| | || |   | ||  ||||||     | |  |||   |||| |  |||||   || || |         | ||||| ||||   |  ||||||   | ||||||| |||||||| ||||| |||||||||||||||||| |||| ||||||||||| || ||||| ||  ||||||||||  |||| ||| | ||||| |
gtgatcacttgt-taaacaatttatgttcagtataataatctataatgcatcaatcttttcaaccacatactgcaaaagtttccttattttttactgctatttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCATCTGTTAGAAAAACAAATAGATTGGTGACCATTGAGGAAAGCTTCCCAC

upper sequence: GRMZM2G097226_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 11
gtaattccttttgtagatgttatactttcagttgttcagtatagccatctagtttttccata-tgccatctgtagtaccttacttttggttcatatttgttg----acagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCC
                  || | |||||   || |   | |    |  |   |||| | | |    ||| ||   || | || |  ||  | || ||  |      | |||| || ||  | || |||||| | || |||||| || |  | || ||||| |||||||||||||||||| |  ||||||| |||||||||||||| || |
------------------gtaaaactttagtttataatgaactttccccctcttttgcaaaaacttcatttgggttatcataatggtgagtgatgttcttatccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTC

upper sequence: GRMZM2G097226_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 11
gtaattccttttgtagatgttatactttcagttgttcagtatagccatctagtttttcc-atatgccatctgtagtaccttacttttggttcatatt--tgttgaca--gGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCC
                  || | || ||   || |   | |   ||  |   |||| |  | |   ||| ||   ||   || |  ||  | || ||  |||  |||  ||| || ||  | || |||||| | ||||||||| || |  | || ||| | |||||||||||||||||| |  ||||||| |||||||||||||| || |
------------------gtaaaacattagtttataatgaacttccccccttttttgcagaaacttcatttgggttatgatagtggtgagtgatgttcttgtccacacagGTCATTAATTTGCGTTCAATCCGGCCACTTGATCGATCCACAATCAATACTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTC

upper sequence: GRMZM2G097226_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA14G02380.1 (Glycine max), 3'ss of exon 11
gtaattccttttgtagatgttatactttcagttgttcagtatagccatctagtttttccatatgc--catctgtagtaccttacttttggttcatatt--tgttgaca--gGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCC
                  || | |||||   ||||   | |   ||  ||  ||||| || | ||  ||| ||   ||   || |  ||  | ||  |  | |  |||  ||| || ||  | || |||||| |||| |||||| |  |  | || ||| | |||||||||||||||||| |  ||||||| |||||||||||||| || |
------------------gtaaaactttagtttgtaatgaacttcc-cctcttttttgcaaaagcatcatttgggttatgataatggtgagtgatgctcttatccacatagGTCATTAATTTGCGTTCAATCCGACCGCTTGATCGGTCCACAATCAATACTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTC

upper sequence: GRMZM2G097226_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 11
---------------------gtaattccttttgta--gatgttatactttcagttgttcagtatagccatctagtttttccatatgccatctgtagtaccttacttttggttcatatttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCC
                      | |||   ||||||  |   | | ||    ||| |||  | |    ||   || | ||||||      | |   | |    | | |||  |  | |||| | |||||| || || ||||| |||||| | || ||||| ||| | || || ||||| || ||||||||||| | | || |||||||||||||||| |||||||| |
gtaactcaaaagaagtttgaaattattttctttgtattggattcagacaactagtagttttggaagttcagaaaggtattccattcagtttttaaggaaagcaattgttg--ttctgtttgat-acagGTTATAAATCTTCGCTCAATCCGTCCCCTTGACAGATCGGCAATCAATGCTTCAGTCAGGAAAACTAGCAGACTGGTGACTGTTGAAGAGGGGTTCCCTC

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|32802035|gb|CD954271.1|CD954271
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTA
EST: gi|32829636|gb|CD969314.1|CD969314
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|211317947|gb|FL318710.1|FL318710
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|32829111|gb|CD968789.1|CD968789
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|60343110|gb|DN210083.1|DN210083
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|211088145|gb|FL307530.1|FL307530
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAT                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttttccatatgccatctgtagtaccttacttttggttcatatttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCC
                         accttac  putative branch site (score: 3)
                                      ttcatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattccttttgtagatgttatactttcagttgttcagtatagccatctagtttttccatatgccatctgtagtaccttacttttggttcatatttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG