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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttccctcatttctgctgctttggccgtgcttatccatcaacttaccacactttgacttaagacattttaatattttcttgtctttggtctgat...

Basic information

species Zea mays
transcript GRMZM2G366935_T07
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G366935_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g40840.1 (Oryza sativa), 5'ss of exon 11
TGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttccctcatttctgctgctttggccgtgct-tatccatcaacttaccacactttgacttaagacattttaatattttcttgtctttggtctgat
 |||||||||||||| ||  | | | | ||| ||||||||||||||||||||||||||||||| || |||||||| || || ||||| ||||| ||||||||||| ||||||||| || ||   ||||     ||||   |  |||  |   | | | | |  ||  | |  |   || | | |  ||  | |   ||| |
AGCTCAGAAATATTTTAGACGAGGAGCGCGTCTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAGAGTATCAGAGCAGTCAAAAAACTAGATCGGCTAAAGgttttggttccctcaattatgtctctttttttttgctacgtttatccccaatctaaattatatctctaaaattcaaaacaatattatgcatatt-cctgtt

upper sequence: GRMZM2G366935_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 5'ss of exon 11
TGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttccctcatttctgctgctttggccgtgcttatccatcaacttaccacactttgacttaagacattttaatattttcttgtctttggtctgat----
|| | | || ||||||||| | | | |||| || |||||||||||||| || ||||| || ||||| |||||||| |||||||| || || || || ||||||  |   |  |   | || |||| || |   |   ||  | | || || ||||  ||    |  | |  ||||| ||   | |  | |  |||   ||    
TGTTGAAAAGTATTTCAGGGGAGGATCACGGTTGAATTGGCCTGAAGGAGCAGTTTCTAGGGAAAGTATCAGAGCAGTGAAGAAGCTTGACCGTCTGAAGgttcca--ccattttctccttctgcctttgatttcaataaacctgaagtt-ccacttttctggt--acattttttagtaaactgt-atgtccggta-aatgcag
















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|71766680|gb|DR964617.1|DR964617
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
EST: gi|76915207|gb|DV165881.1|DV165881
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
EST: gi|24765506|gb|CA400665.1|CA400665
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCCGAGCTGGCAGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
EST: gi|71760328|gb|DR958265.1|DR958265
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
EST: gi|5607698|gb|AI901365.1|AI901365
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
EST: gi|71426269|gb|DR807319.1|DR807319
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
EST: gi|60345840|gb|DN212813.1|DN212813
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCCGAGCTGGCAGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
EST: gi|166490845|gb|EG161148.1|EG161148
EST:     AGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGC
genomic: AGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGC
EST: gi|74242829|gb|DT650743.1|DT650743
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
EST: gi|71775054|gb|DR972932.1|DR972932
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttccctcatttctgctgctttggccgtgcttatccatcaacttaccacactttgacttaagacattttaatattttcttgtctttggtctgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA