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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC

Basic information

species Zea mays
transcript GRMZM2G178998_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G00760.1 (Glycine max), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagc-tcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
||||| ||| | || || || || || |||| || ||| || || || || | | ||| || | | || || | | | || | | ||| | ||||| || |||| ||||| || || || ||||||||||| ||||| || || |||||||| ||||| || |||||||| || |||||||| |
-----------------------------------------------------gtagtact-gatcgagttcatagcatctaaattca-----agagggacaattttattggtgaaagat-atatattatttgttaac--ttcttcatttttttttcttttttgtttttaaattttaa------agAGATTTGCAGAATAGGAACAGAAGAACAAAATGAATGGTACTTCTTTAGCCATAAAGATAAGAAGTATCCAACTGGAACTCGCACGAATAGAGCGACTGC

upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G36600.1 (Glycine max), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
|| | || || | | | || | | |||| | || | ||| | | | || | | | | | || | | | | | | | ||| | ||||| || ||| |||||||| || || ||||||||||| ||||| || || |||||||| ||||| || |||||||| || ||||| || |
---------------------------------------------------------------------gta-gaactgatcgagttcaattcatagcatctaaattctagaggggcgattttattggtgaaagatatattgttaactttgcattgtttttttcttttcgttttaaattttaaagAGATTTGCAGAATAGGAGCAGAAGAGCAAAATGAATGGTACTTCTTTAGCCATAAAGATAAGAAGTATCCAACTGGAACTCGCACAAATAGAGCAACTGC

upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G47680.1 (Glycine max), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttat-aagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
| | | ||| || | || | | || | || | | | || || | || ||| | | || | | ||| ||||| || ||| ||||||| || || ||||||||||| ||||| || || |||||||| ||||| || |||||||| || ||||| || |
------------------------------------------------------------------------------------ttagtttatagaatt-taaaatcaacatgaaataatattatttgtaaacgatatatcattaattttttggcttcctttcttctttttttgaaaatatga-agAGCTTTGCAGAATAGGAGCACAAGAGCAAAATGAATGGTACTTCTTTAGCCATAAAGATAAGAAGTATCCAACTGGAACTCGCACAAATAGAGCAACAGC

upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G12260.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
| || | || | || | | | | || | | || | | | || || || | ||| | | || |||| ||| ||||| ||||| |||||||||| || ||||||||||| ||||| || ||||||||||| || || || ||||| ||||| ||||| || |
-------------------------------------------------------------------------------------gtttgcccaatcccaccatctctatccttcattactttgtctctatttcctaaggaaagattttaaaagtctttttt---tattcgtt-tgtggaaatagAGTTGTGCAAAATTGGGCATGAAGAGCAGAGTGATTGGTACTTCTTTAGCCATAAAGACAAGAAGTATCCCACAGGGACTCGAACCAATAGAGCAACAAA

upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
| | || | | | | | | | | | | | | | ||||| | ||| || ||| ||| || | | | | | | |||| | ||| |||| ||| |||| ||||||||||| ||| ||||||||||| || || || ||||||||||| || || || ||||| ||||| ||||| ||||
---------------------------------------------------------------gtttag-caggaaaatcctatcatctctctttagtagtgatatccttgt---tttggtataaattaaggcttacgattgt------------------tgttttttctttgtgataatttagAGTTATGCAAGATAGGAAACGAAGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA

upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0154g00020.t01 (Vitis vinifera), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagc-atgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacg-gttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
||| ||||| || |||| | | ||| | |||| || | || | || || ||||| | | | | |||| || ||| | | | ||| | | || ||| |||| || || | ||||||||||| |||||||| ||||| ||||| || || |||||||| ||||| || ||||| || || ||||| || |
--------------------------------------------------------gtatgtagctcttattcctacagtccttccctatgcatacaacagaaaa-----tatgta--tatcttg-atgaaatactatgcatcataaaat-ctgacttccatgttcatttttctta-atttgaatagAGTTATGCAAAATAGGCACTGAAGAGCAGAATGAGTGGTATTTCTTTAGCCATAAAGATAAGAAGTATCCAACTGGAACTCGAACTAATAGAGCTACAAA

upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
--gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaac--ggttataagccgctaactcacttctacatatg--catggtgacgaaa-cagAAAAGTGCAGGATTGGAAGCGA------AGAG---CAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
||| | | || | |||||| | | | |||| ||| | | || || || || || | | | || || | || | | | ||| | || | | | || || ||| | | | || | | ||||| |||||||||||| ||| |||| || ||||| |||||||||||||||||||| ||||| |||||||| | |||| ||| | ||| |
gtaagaatcgatcagaatcctcggtgtactatg----tatgacaccagactagaaaacacgtcctcacatgcttcgt-tgccccatttca-gtctattaagattgaactcatggtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccgatgtggtcatcagAAGTGTGCAGGATTGGGGACGACCCACCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG---------

upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S102_187V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgt--acttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC-
||| || || | || || |||| | || || | | | | || || ||| | | || || | | || | || | || | | | | ||| | | | | | | | |||||| |||| || ||||||||||||||||||||||| ||||| || || ||| | || | || |||| || |
----------------------------------------------gcatgaacatgctcatttgaaggacatatttgagtttcgaa-tttctcccacatagagtttttgttttgggattggtggatat----cttgatactgatga-----tattcaatttttgtggcgatgtcaggggtatgcagGATCGGGGACG-TCACCACCGAAGACCAGAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAATATCCTTGCGGGAACCGTGCAAATCGAGCCACCGCC

upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatg-tacacctcaaagcatgtgtggaacaacaagcttct-tgtggagtcat-tatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAG---------AGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
||| |||| | | | |||| | | || | | | | | | | | ||| | | | | || | | || | | | | | | | | | | | || ||| |||| | | || | | |||| | | ||| | ||| || ||| | |||| |||||| ||||| ||| | | |||| ||| ||||||||||||||||||||||||||||| || || || || | ||| | ||| |
gtaagccaacgaacccacattttgca----ggatttcattaacgttggttgaggttagaa--aactggaactcgctttagttcgaggaatatataaatagatatggatatatatatatatatatatatatgagaatactc---taagtactgataacac-catctgtacttgc--ggcgac--atcagAGGTGTGCAGAATTGGCGACGACGCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG---------

upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtg-acgaaacagAAAAGTGCAGGATTGGAAGCGA------AGAGCA---GAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
| | || || | | || || ||| | | | ||| || | | | | | |||| || | || |||| | ||||| || | || | | | | | || | | | ||| | | || || || | ||||| ||||||||| || ||| |||||| | || ||||||||||||||||||||||| |||||||| || || || | || ||||| |
gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaaca-gtactatccattgaat-tgtg-atcaacataag-ctcaagagcatgttctcctcatctattgatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG---------

upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGG-ATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
|||| |||| | || || | || | || |||| | ||| | || ||||||| | | | ||| | | | || | | |||| || | |||||| | ||||||||||| ||||| ||||||||||||||||| ||||||| ||| ||||| |
----------------------------------------------------------------gcaagatcatcacactcaagtgccaacctgaagca--------cgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagc-----gtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------

upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaag----catgtgtggaacaacaagc--ttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaa-acagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
| ||| | |||||| ||| | | || || || | ||||| | |||| || | || || | | | | || ||| | || | || || | | |||||| |||| | ||||| || |||||| ||||||||||||||||||||||||| |||||||| ||||| ||||| || | ||||||||||| ||
----------------------------------------------------------------gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgtt-----ctaaatgtctct---tctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG

upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
| || |||| | | ||| | | | | || | || || || | | | | | | | | |||| ||||| | ||| ||| | || || | ||| |||||||| ||||| ||||||||||||||||| || || || ||||||||||||||||| || |
-----------------------------------------------------------------------------------------------------------gtagtctagtc-tcctccatttcgat--atgattgcacaccactgacacctctttcattgttcttcg-attttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC

upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaa-acagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
||| || || | || | || | | | || || | ||||| | |||| || | || || | | | | || ||| | || | || || | | |||||| |||| | ||||| || |||||| ||||||||||||||||||||||||| |||||||| ||||| ||||| || | ||||||||||| ||
------------------------------------------------gtaagacggtcatccctcaag---------cttctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgtt-----ctaaatgtctct---tctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG

upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
| || |||| | | ||| | | | ||| | || || || | | | | | | | | |||| ||||| | ||| ||| | || || | ||| |||||||| ||||| ||||||||||||||||| || || || ||||||||||||||||| || |
-----------------------------------------------------------------------------------------------------------gtagtctagtc-tcctccatttcgac--atgattacacaccactgacacctctttcattgttcttcg-attttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC

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|149106166|gb|EE291854.2|EE291854
EST:     TGTGATAAAAGATGTGGATTTGTACAAGATTGAGCCTTGGGATCTGCAAG                         AAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCC
genomic: TGTGATAAAAGATGTGGATTTGTACAAGATTGAGCCTTGGGATCTGCAAGgtacatcaac ... gacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
                     aactcac  putative branch site (score: 2)
 ttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT