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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttctcagcacgcaagcctggctgttccggtggtattgtggcagaatgattaaggcataggtgattgtgctgcctgttactaattcattctgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAGCAGCAGGATGCTCTGCCAAAGCATGCTAATTCGGTACTCCTTGCTGCTG

Basic information

species Zea mays
transcript GRMZM2G023232_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023232_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g08840.1 (Oryza sativa), 3'ss of exon 7
gttctcagcacgcaagcctggctgttccggtggtattgtggcagaatgattaaggcataggtgattgtgctgcct-gttactaattcat-tctgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAGCAGCAGGATGCTCTGCCAAAGCATGCTAATTCGGTACTCCTTGCTGCTG
 || | |  | ||    || | | ||    | ||    ||| || |  |       ||   |||| ||  |     | | |||||  |  | | | |  |||||| |  ||||||||||||| || ||||  ||||||||||||||| ||||||||||||||||||| |||||||||||| || | || ||| |     |||
tttgttaatatgcct-tctagttcttgtttttgtga-atggtagtagcaaaggaatattaatgatcgttttcttcagctgctaatcaaaatttctgcatcagGTCCTGGATGAGTGTTCGGAGGCCGAGATCTGGCTAATAGAGAAACAGCAGCAGCAGGATGCTCTACCAAAGCATGCTGATCCTGTCCTCTTAATATCTG
















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|211440101|gb|FK975188.1|FK975188
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|5688777|gb|AI941792.1|AI941792
EST:     ATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: ATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|21391185|gb|BQ529234.1|BQ529234
EST:     CGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: CGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|4647591|gb|AI622666.1|AI622666
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|67032981|gb|CO461730.1|CO461730
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|18661122|gb|BM501223.1|BM501223
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|32843014|gb|CD982695.1|CD982695
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|60394852|gb|DN227721.1|DN227721
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|20803202|gb|BQ294252.1|BQ294252
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|24768622|gb|CA403751.1|CA403751
EST:     CGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: CGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|37375721|gb|CF624316.1|CF624316
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|83278270|gb|DV942278.1|DV942278
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|61119613|gb|DN560574.1|DN560574
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|211139744|gb|FL308469.1|FL308469
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|60354460|gb|DN221433.1|DN221433
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|4624362|gb|AI615195.1|AI615195
EST:     GTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: GTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|32932457|gb|CF037269.1|CF037269
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|67034483|gb|CO463033.1|CO463033
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|6022408|gb|AW067336.1|AW067336
EST:     ATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: ATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|213174387|gb|FM187872.1|FM187872
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTNNNCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
EST: gi|33098111|gb|CF058071.1|CF058071
EST:     AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAG                         GTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG
genomic: AGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 526

TGCTGTTAGCCAACTGGTATACTGCATCAATAGCTTCAGAGAAGCTGCACAGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAGCAGCAGGATGCTCTGCCAAAGCATGCTAATTCGGTACTCCTTGCTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 243

TGCTGTTAGCCAACTGGTATACTGCATCAATAGCTTCAGAGAAGCTGCACAGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAGCAGCAGGATGCTCTGCCAAAGCATGCTAATTCGGTACTCCTTGCTGCTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 297

TGCTGTTAGCCAACTGGTATACTGCATCAATAGCTTCAGAGAAGCTGCACAGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAGCAGCAGGATGCTCTGCCAAAGCATGCTAATTCGGTACTCCTTGCTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

TGCTGTTAGCCAACTGGTATACTGCATCAATAGCTTCAGAGAAGCTGCACAGTCTACCGACCAGAAGTTTGAACACATAGACATGTCAGAAAAGCGAAAGgtatatttgt ... tgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAGCAGCAGGATGCTCTGCCAAAGCATGCTAATTCGGTACTCCTTGCTGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgattaaggcataggtgattgtgctgcctgttactaattcattctgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAGCAGCAGGATGCTCTGCCAAAGCATGCTAATTCGGTACTCCTTGCTGCTG
                                tactaat  putative branch site (score: 327)
                                          ttctgttct  putative PPT
                               ttactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctcagcacgcaagcctggctgttccggtggtattgtggcagaatgattaaggcataggtgattgtgctgcctgttactaattcattctgttctacagGTCATTAATGAGTGTTCGGAAGCAGAGACTTGGCTAATAGAGAAAAAGCAGCAGCAGGATGCTCTGCCAAAGCATGCTAATTCGGTACTCCTTGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - -gcacgca
- - - - - - - - - - gctgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttact