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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataacacttcatttgttttctcaccatcaatctcaagggtttactccaactatttagccacttattgcattccttgtgatacttcattgctgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGTGACAGGAGCAGCCAAGAAGCAGGCGAAGGAGAAGACACCTAATAGTAGC

Basic information

species Zea mays
transcript GRMZM2G172001_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G172001_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g66420.1 (Oryza sativa), 3'ss of exon 3
--ataacacttcatttgttttctcaccatcaatctcaagggtttactccaactatttagccacttattgcattccttgtgatacttcattgctgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGTGACAGGAGCAGCCAAGAAGCAGGCGAAGGAGAAGACACCTAATAGTAGC
   | | |   |   ||| |   |||   | || | |      || | ||    |     ||||  |    | | || || | || |  |  | | ||||||||||||||||||||   ||||||||||  |||| || ||||||||||||||||||||||| || |||||||||||||| || ||||| || || ||||| 
ttcttagaaaactgctgtctggccactggctattttatc--cctagttcaggcttgcttgcactcctaagttacattttggttctactattttcttatgcagGAGGCGACTCTTTAATATGATAAACAATTTGCCAACAATATTTGAGGTAGTGACAGGAGCCGCTAAGAAGCAGGCGAAAGAAAAGACTCCCAACAGTAGT
















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|60397867|gb|DN230683.1|DN230683
EST:     TCTGTTGCATTCTACTTTGGTGCACGGTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|211502673|gb|FL086824.1|FL086824
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGAT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGAT
EST: gi|149042113|gb|EE047091.2|EE047091
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|211505027|gb|FL086835.1|FL086835
EST:     TCTGTTGCATTCTACKTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTT
EST: gi|76921025|gb|DV168421.1|DV168421
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|78077036|gb|DV505470.1|DV505470
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|71436584|gb|DR817634.1|DR817634
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|22935540|gb|BU571815.1|BU571815
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|211166632|gb|FK973167.1|FK973167
EST:     TTTGGTGCACGGTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|71426022|gb|DR807072.1|DR807072
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|26560007|gb|CA832242.1|CA832242
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|211507394|gb|FL086856.1|FL086856
EST:     TCTGTTGCATTCTACTTTGGTGCACGGTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATT
EST: gi|87157435|gb|DY402224.1|DY402224
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|78110540|gb|DV528950.1|DV528950
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|74241423|gb|DT649337.1|DT649337
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|71438530|gb|DR819580.1|DR819580
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|78110698|gb|DV529096.1|DV529096
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|71435348|gb|DR816398.1|DR816398
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|149108563|gb|EE292842.2|EE292842
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|74237049|gb|DT644963.1|DT644963
EST:     ACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: ACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|94480407|gb|EB709365.1|EB709365
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|74243375|gb|DT651289.1|DT651289
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|74237050|gb|DT644964.1|DT644964
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
EST: gi|15177432|gb|BI398386.1|BI398386
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAG
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAG
EST: gi|5555374|gb|AI881325.1|AI881325
EST:     TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAG                         GAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT
genomic: TCTGTTGCATTCTACTTTGGTGCACGCTTTGGATTTGACAGAGAAACTAGgtaattcttc ... tgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaactatttagccacttattgcattccttgtgatacttcattgctgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGTGACAGGAGCAGCCAAGAAGCAGGCGAAGGAGAAGACACCTAATAGTAGC
     tattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataacacttcatttgttttctcaccatcaatctcaagggtttactccaactatttagccacttattgcattccttgtgatacttcattgctgtaatgcagGAGGCGACTCTTTAGCCTGATAAACAACATGCCCACGATATTTGAGGTAGTGACAGGAGCAGCCAAGAAGCAGGCGAAGGAGAAGACACCTAATAGTAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - cacttca
- - - - - - - - - - -caccatc
- - - - - - - - - - - - - - - - - - - - - - -ccaacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatact