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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaatctaatgctggatctggatggacgtctcagtctcatctaccgtgtgtacgttttgagttttgacagagggaggtatattgtatatacacctgcagGGCTCAGGTGGTGGGATGGCCACCGGTCCGGTCGTTCCGGAAGAACATCATGTCCGTGCAGTCCGACAAGGGCGCCGCCGCCGCCAACGGCGACAAGTCC

Basic information

species Zea mays
transcript GRMZM2G138268_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g40890.1 (Oryza sativa), 3'ss of exon 1
ataaatctaatgctggatctggatggacgtctcagtctcatctaccgtgtgtacgttttgagttttgacagagggaggtatattg--tatatacacct-gcagGGCTCAGGTGGTGGGATGGCCACCGGTCCGGTCGTTCCGGAAGAACATCATGTCCGTGCAGTCCGACAAGGGCGCCGCCGCCGCCAACGGCGACAAGTCC
 | | |   ||  | | |    ||  |      ||   | ||||     |      | | | || | |    | ||   | ||||  || ||   | |  |||||| |||||||| || ||||| ||||||||||| | ||||||||||||| || |||||||| |||||||||||   | ||||||| |||||| |     |
-tcagtaagatatttggtaataat--attatagagctacttctagtaactagctactcttaattattaatcggtgaaaaaaattggttaaatcttcttcacagGGCACAGGTGGTTGGGTGGCCGCCGGTCCGGTCATACCGGAAGAACATCCTGGCCGTGCAGGCCGACAAGGGCAAGGACGCCGCCGACGGCGGCGGCGAC

upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g43400.1 (Oryza sativa), 3'ss of exon 1
ataaatctaatgctggatctggatggacgtctcagtctcatctaccgtg-tgt-acgttttgagttttgacagagggaggtatattgtatatacacctg-cagGGCTCAGGTGGTGGGATGGCCACCGGTCCGGTCGTTCCGGAAGAACATCATGTCCGTGCAGTCCGACAAGGGCGCCGCCGCCGCCAACGGCGA-CAAGTCC---
 || ||  |   |   ||    |   || |  |    | | | ||  || ||| |  |||| | |  | |   |   |   | | || |||||   |   |||||| ||||||||||| ||||| ||||||||||||||| |||||||| |  |  ||| | | | | |    |||| || ||| |   | || || || |  |   
ttagatagatctcaccattaaaa---acctaactagttgagcgacgatgatgtcaacttttcattgattaattaattaatcagaatgcatatatgtcgatcagGGCGCAGGTGGTGGGGTGGCCGCCGGTCCGGTCGTTCAGGAAGAACGTGCTCGCCGAGAAATGCAA----GGCGGCGGCGCTGGTGAAGGTGAGCATGGACGGC

upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G34380.1 (Glycine max), 3'ss of exon 1
ataaatctaatgctggatctggatggacgtctcagtctcatctaccgtgtgtacgttttgagttttgacagagggaggtatattgt---atatacacctgcagGGCTCAGGTGGTGGGATGGCCACCGGTCCGGTCGTTCCGGAAGAACATCATGTCCGTGCAGTCCGACAAGGGCGCCGCCGCCGCCAACGGCGACAAGTCC
   ||  || |      ||   ||     |  ||      |  |   || |||    |||| |  | | | |   ||  ||||||     |  | |  || ||| | ||||||||||| |||||||| || ||||| ||||||||||||||  || | |||||      |   || |  |    ||  ||   |  ||   | 
--taacttattttaacttcgttatatgattaccatatatgttcatgatgcgtattaattga-tcataatatataaagtgatattgatgagttgaaatgtgtagGACGCAGGTGGTGGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTTGGCTGTGCAAAAGAGCGTTGGAGAAGAGAGCGAGAAGAACAGCAGCCCT

upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G31530.1 (Glycine max), 3'ss of exon 1
ataaatctaatgctggatctggatggacgtctcagtct---catctaccgtgtgtacgttttgagttttgacagagggaggtatattgtatatac--acctgcagGGCTCAGGTGGTGGGATGGCCACCGGTCCGGTCGTTCCGGAAGAACATCATGTCCGTGCAGTCCGACAAGGGCGCCGCCGCCGCCAACGGCGACAAGTCC
     || | ||||| || |      |  ||||  ||     |  ||||   | |   |  | |  | | |   |  ||| |  | || |  |    |  || ||||| |||||||| || |||||||| || ||||| ||||||||||||||  |  | || ||      |   || |  |    ||  ||   |  ||    |
----ttcaagtgctgtat-taatcttatatctccttcaacataattaccacatattgatgataatatataaagtaatgagttgaaatgaaattggtgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTTAGCTGTACAAAAGAGCGTCGGAGAAGAGAACGAGAAGAACAGCAGCAGC

upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G16080.1 (Glycine max), 3'ss of exon 1
ataaatctaatgctgg-atctggatgga--cgtctcagtctcatctaccgtgtgtacgttttgagttttgacagagggaggtatattgtatatacacctgcagGGCTCAGGTGGTGGGATGGCCACCGGTCCGGTCGTTCCGGAAGAACATCATGTCCGTGCAGTCCGACAAGGGCGCCGCCGCCGCCAACGGCGACAAGTCC------
 ||| | || |      || || ||     | || |   | | |||| | | || |    ||        |   | | |   | |    ||  |||| |  ||||| || ||||||||||||||||| ||  |||| |||||||||||||   ||| ||  ||| || | ||| ||  || ||  |   |  |||| |||  |      
-taattttagtttcattatatgcataattccatccccaacccctctaac-tatgaagtgattatacgaatattaatgaatcaaaacaaaatgaacactt-tagGGCGCAAGTGGTGGGATGGCCACCCGTGAGGTCTTTCCGGAAGAACA---TGTTCG--CAGCCCAA-AAGAGCAGCGGCGGAGAGGAAAGCGAAAAGAGCAGCCCT

upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G03720.2 (Glycine max), 3'ss of exon 1
ataaatctaatgctggatctggatggacgtctcagtctcatctaccgtgt-gtacgttttgagttttgacagagggaggtatattgtat----atacac-ctgcagGGCTCAGGTGGTGGGATGGCCACCGGTCCGGTCGTTCCGGAAGAACATCATGTCCGTGCAGTCCGACAAGGGCGCCGCCGCCGCCAACGGCGACAAGTCC------
     | | ||  |     |   |  |   | ||  | |  | |   ||  ||   |   | | ||| ||  |      |  |||  |     ||  ||  |  ||||| || ||||||||||||||||| ||  |||| ||||||||||||||  |     ||||| || | ||| ||  || ||  |   |  |||| |||  |      
-----tttcattatatgcataatttcat-ccccaacccctccaattatgaagtgaatcaagtgattttacgaatattaatgaattaaaacaaaatgaacattttagGGCGCAAGTGGTGGGATGGCCACCTGTAAGGTCTTTCCGGAAGAACATGTT-----TGCAGCCCAA-AAGAGCAGCGGCGGAGAGGAAAGCGAGAAGAACAGCCCT

upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G04730.1 (Arabidopsis thaliana), 3'ss of exon 1
--ataaatctaatg-ctggatc-tggatggacgtctcagtctcatctaccgtgtgtacgttttgagttttgacagagggaggtatattgtatatacacctgcagGGCTCAGGTGGTGGGATGGCCACCGGTCCGGTCGTTCCGGAAGAACATCATGTCCGTGCAGT--CCGACAAG-GGCGCCGCCGCCGCCAACGGCGACAAGTCC
  |    |  ||   || |||| |  |   || | | |     |      ||   |  || ||   ||   |   |   |   | ||  | ||   |  | |||||| || || ||||||||||||||||| || || ||||| |||||| |||||||||  ||    ||||| |  || |  ||| |||       ||| |||   
acacgtgtagaacaactagatcatttacaaacattttacaaaaaaaagaagta-atgagtatta--ttgaaattaaaaaaaaaaaatcat-tacgaaatttcagGGCACAAGTTGTGGGATGGCCACCGGTACGATCTTTCCGCAAGAACGTCATGTCCGGCCAAAAACCGACCACCGGAGATGCCACCGAAGGAAACGATAAG---

upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv07s0141g00290.t01 (Vitis vinifera), 3'ss of exon 1
ataaatctaatgctggatctggatggacgtct--cagtctcatctaccgtgtgtacgttttgagttttgacagaggga-ggtatattgtatatacacctgcagGGCTCAGGTGGTGGGATGGCCACCGGTCCGGTCGTTCCGGAAGAACATCATGTCCGTGCAGTCCGACAAGGGCGCCGCCGCCGCCAACGGCGACAAGTCC
     | |  || |  |    | ||  |   |   |   ||||  ||       |    |  |  |    |||  | |   |  || | |  |  |  |  ||||| ||||| ||||| ||||||||||| ||||| ||||||||||||||  || ||| ||||   | |    |||  |  |  |  || |    |     |
---tttttcctgttaaaaacagttgttctcataataaagtcattaactaaaaccatacataaaaataaagcaggtgaataattcatggaaattggaattttagGGCACAGGTTGTGGGGTGGCCACCGGTTCGGTCCTTCCGGAAGAACATGTTGGCCGGGCAGAAGGGCGGCAGCGAGGAAGGGGAGAAGGTGAGCTGCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgtgtacgttttgagttttgacagagggaggtatattgtatatacacctgcagGGCTCAGGTGGTGGGATGGCCACCGGTCCGGTCGTTCCGGAAGAACATCATGTCCGTGCAGTCCGACAAGGGCGCCGCCGCCGCCAACGGCGACAAGTCC
                 ttttgac  putative branch site (score: 3)
                                 tatattgtatataca  TA-rich tract