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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtagacttgtacgaagactttccgcgcaaatgtccttctgcattactgactatttccatattggccgtaacaatgtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG

Basic information

species Zea mays
transcript GRMZM2G042027_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042027_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g29860.3 (Oryza sativa), 3'ss of exon 9
------------------gtgtagacttgtacgaagactttccgcgcaaatgtccttctgcattactgactatttccatattggccgtaacaatgtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG
                     |  |     |  |  ||    |   |   |   |  |||      |  ||    ||||||    | |   |  | ||  |||||||  || |||||| ||| | |||||||||||||| || ||||||||||| || |||||||| |||  |||||||||||||
gtggatccttttgtatcaaaatccatccacagaataacacatcattcctttcaacccctgttggtatcgctgaccccatatatttctttggaccgcaatcgcagGGATCAGCGAACCAGTACTCCGGAATTGTAAGCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAG
















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|78092776|gb|DV521150.1|DV521150
EST:     GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG                         GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
genomic: GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAGgtgtagactt ... gtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
EST: gi|28984641|gb|BQ539144.2|BQ539144
EST:     GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG                         GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
genomic: GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAGgtgtagactt ... gtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
EST: gi|113702185|gb|EE679689.1|EE679689
EST:     GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG                         GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
genomic: GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAGgtgtagactt ... gtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
EST: gi|113702087|gb|EE679591.1|EE679591
EST:     GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG                         GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
genomic: GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAGgtgtagactt ... gtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
EST: gi|76011416|gb|DT938586.1|DT938586
EST:     GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG                         GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
genomic: GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAGgtgtagactt ... gtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
EST: gi|71302081|gb|DR787128.1|DR787128
EST:     GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG                         GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
genomic: GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAGgtgtagactt ... gtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
EST: gi|16918359|gb|BM073712.1|BM073712
EST:     GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG                         GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
genomic: GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAGgtgtagactt ... gtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
EST: gi|211226520|gb|FL435621.1|FL435621
EST:     GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG                         GGACAAGGGAACCAATACACTGGAATTGTAATCTGTGCTCAGACAATCCTC
genomic: GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAGgtgtagactt ... gtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
EST: gi|91056577|gb|EB166995.1|EB166995
EST:     GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG                         GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGTTCAGACAATCCTC
genomic: GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAGgtgtagactt ... gtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
EST: gi|33092443|gb|CF052437.1|CF052437
EST:     GAGCTATAACAACCCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG                         GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
genomic: GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAGgtgtagactt ... gtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
EST: gi|50325363|gb|CO520489.1|CO520489
EST:     GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG                         GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
genomic: GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAGgtgtagactt ... gtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
EST: gi|67018887|gb|CO447636.1|CO447636
EST:     GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG                         GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC
genomic: GAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAGgtgtagactt ... gtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtccttctgcattactgactatttccatattggccgtaacaatgtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG
                   actattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtagacttgtacgaagactttccgcgcaaatgtccttctgcattactgactatttccatattggccgtaacaatgtaactgcagGGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG