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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATAAAGTTGTGCCGGAGAAGAAAGTTCTTGAAGTGGTAGTTGAGAAAGGTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactccttagtcctcagttctaaagttattcctctggcacaaactaaacttctgttctaactaatgtgtgcaaccttgggttctaactatgttgtgctcgtgtgcag

Basic information

species Zea mays
transcript GRMZM2G028218_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028218_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA12G10150.2 (Glycine max), 5'ss of exon 4
TGATAAAGTTGTGCCGGAGAAGAAAGTTCTTGAAGTGGTAGTTGAGAAAGGTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactccttagtcctcagttctaaagttattcctctggcacaaactaaacttctgttctaactaatgtgtgcaaccttgggttctaactatgttgtgctcgtgtgcag
 || || ||||||| |||||||||||| ||||||||  | || || || || |||||||||||||||||||| |||||||||||||||||||||||||||||| ||      |     |||||  |  | ||     | ||   ||   |  | | | |   |   |||||     | || || ||| |   ||| |||             
AGAGAAGGTTGTGCAGGAGAAGAAAGTCCTTGAAGTTATTGTAGAAAAGGGGATGCAGAATGGGCAGAAGATAACATTCCCTGGCGAAGCTGATGAAGCGgta-tgttgatatgagaatcagtattgtaatttgcattgtgcttca---tggattgcagaaatttataatg-----acccatgagttgttggtattttgcag----------

upper sequence: GRMZM2G028218_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA13G38790.1 (Glycine max), 5'ss of exon 4
TGATAAAGTTGTGCCGGAGAAGAAAGTTCTTGAAGTGGTAGTTGAGAAAGGTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactccttagtcctcagttctaaagttattcctctggcacaaactaaacttctgttctaactaatgtgtgcaaccttgggttctaactatgttgtgctcgtgtgcag
 || || ||||| | |||||||||||| |||||||| || || ||||| || ||||||||||| |||||||| ||||||||||| ||||||||||||||||||        ||   | |   | || |   | | ||    |   |    |||||  | ||  | ||| | | ||       |                             
AGAGAAGGTTGTTCAGGAGAAGAAAGTACTTGAAGTTGTTGTGGAGAAGGGAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgta------tgttgagctttgatgctgacactgtacc---agattatggaaaactattttttgagctattttttgttttgcag-----------------------------

upper sequence: GRMZM2G028218_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G17930.1 (Glycine max), 5'ss of exon 4
TGATAAAGTTGTGCCGGAGAAGAAAGTTCTTGAAGTGGTAGTTGAGAAAGGTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactccttagtcctcagttctaaagttattcctctggcacaaactaaacttctgttctaactaatgtgtgcaaccttgggttctaactatgttgtgctcgtgtgcag
 || || ||||||| |||||| ||||| ||||||||  | || || || || |||||||| ||||||||||| ||||||||||||||||||||||||||||||     | || |      | || ||| || |||    | |           ||  ||    |   ||| | |       || ||| |   ||| |||             
AGAAAAGGTTGTGCAGGAGAAAAAAGTCCTTGAAGTTATTGTGGAAAAGGGAATGCAGAACGGGCAGAAGATTACATTCCCTGGCGAAGCTGATGAAGCGgta-----tgctgatatgagaattgtaatgtcatttgcattgtgt--------ctcatggatcacagaatttataatgatctgagttgtttgtattttgcag----------

upper sequence: GRMZM2G028218_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA12G31620.2 (Glycine max), 5'ss of exon 4
TGATAAAGTTGTGCCGGAGAAGAAAGTTCTTGAAGTGGTAGTTGAGAAAGGTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactccttagtcctcagttctaaagttattcctctggcacaaactaaacttctgttctaactaatgtgtgcaaccttgggttctaactatgttgtgctcgtgtgcag
 || |||||||| | |||||||||||| |||||||| || || ||||| || ||||||||||| |||||||| ||||||||||| |||||||||||||| |||       ||| |    ||   |     |   |  |       |  || | |||    | |   |  | ||                                       
AGAGAAAGTTGTTCAGGAGAAGAAAGTACTTGAAGTTGTTGTGGAGAAGGGAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCAgtatgttgagctttgataccaacaccgtgctggattatggaaattaggctgaccttgatctttttttgttttgcag------------------------------------

upper sequence: GRMZM2G028218_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv13s0073g00560.t01 (Vitis vinifera), 5'ss of exon 5
TGATAAAGTTGTGCCGGAGAAGAAAGTTCTTGAAGTGGTAGTTGAGAAAGGTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaat---gactccttagtcct----cagttctaaagttattcctctggc-acaaactaaacttct---gttctaactaatgtgtgcaaccttgggttctaactatgttgtgctcg-tgtgcag----------------------
||| || ||||| |  |||||||||||  | |||||  | || ||||| || ||||| ||||| |||| ||| ||||||||||| ||||||||||||||||| |     | |   || | ||      ||| | ||  | || ||      | |||| || | |||    | ||   |  ||| |  || | |   |||    | ||||||  | | | ||                         
TGAGAAGGTTGTACAAGAGAAGAAAGTGTTGGAAGTCATTGTAGAGAAGGGGATGCAAAATGGACAGAGGATAACATTCCCTGGAGAAGCTGATGAAGCGgtgagtcaaagtgtctaattctatatttgttatcaatctgtttcttcattgataaacaaagcatcttgcatactttttggtgtctataaacata--ttcctcatgtgttgttattgatttgtgagtatgctttgagctccttgcag

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|40336876|gb|CK370946.1|CK370946
EST:     GTATGCAGAACGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCG                         CCTGATACTGCCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
genomic: GTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactc ... tcgtgtgcagCCTGATACTGCCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
EST: gi|67030348|gb|CO459097.1|CO459097
EST:     GTATGCAGAACGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCG                         CCTGATACTGCCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
genomic: GTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactc ... tcgtgtgcagCCTGATACTGCCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
EST: gi|31360427|gb|CD444784.1|CD444784
EST:     GTATGCAGAACGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCG                         CCTGATACTGCCACTGGAGATATTATCTTTGTTCTCCAGCAGAAGGAGCAT
genomic: GTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactc ... tcgtgtgcagCCTGATACTGCCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
EST: gi|32845339|gb|CD985020.1|CD985020
EST:     GTATGCAGAACGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCA                         CCTGATACTACCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
genomic: GTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactc ... tcgtgtgcagCCTGATACTGCCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
EST: gi|33100170|gb|CF060130.1|CF060130
EST:     GTATGCAGAACGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCA                         CCTGATACTACCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
genomic: GTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactc ... tcgtgtgcagCCTGATACTGCCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
EST: gi|67035410|gb|CO463943.1|CO463943
EST:     GTATGCAGAACGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCG                         CCTGATACTGGCACTGGAGATATCATCTTTGNTCTCCAGCAGAAGGAGCAT
genomic: GTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactc ... tcgtgtgcagCCTGATACTGCCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
EST: gi|51592714|gb|CV071860.1|CV071860
EST:     GTATGCAGAACGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCG                         CCTGATACTGCCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
genomic: GTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactc ... tcgtgtgcagCCTGATACTGCCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
EST: gi|32845319|gb|CD985000.1|CD985000
EST:     GTATGCAGAACGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCA                         CCTGATACTACCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
genomic: GTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactc ... tcgtgtgcagCCTGATACTGCCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
EST: gi|67038376|gb|CO464706.1|CO464706
EST:     -TATGCAGAACGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCG                         CCTGATACTGCCACTGGAGA-ATCATCTTNGNTCTCCAGCAGAAGGAGCAT
genomic: GTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactc ... tcgtgtgcagCCTGATACTGCCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
EST: gi|7162265|gb|AW519872.1|AW519872
EST:     GTATGCAGAACGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCG                         CCTGATACTGCCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
genomic: GTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactc ... tcgtgtgcagCCTGATACTGCCACTGGAGATATCATCTTTGTTCTCCAGCAGAAGGAGCAT
EST: gi|32836749|gb|CD976427.1|CD976427
EST:     GTATGCAGAACGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCA                         CCTGATACTACCACT
genomic: GTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactc ... tcgtgtgcagCCTGATACTGCCACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATAAAGTTGTGCCGGAGAAGAAAGTTCTTGAAGTGGTAGTTGAGAAAGGTATGCAGAATGGGCAGAAGATCACATTCCCTGGCGAAGCTGATGAAGCGgtaatgactccttagtcctcagttctaaagttattcctctggcacaaactaaacttctgttctaactaatgtgtgcaaccttgggttctaactatgttgtgctcgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC