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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgttcaacatactcaccagttctgttttagtggcaataaacttgctcagtaccgcagggaggctgttactttgtctaatgttgttgcgattcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGTGGCTAGTGTATTGGAGAAGAACAACTTGCCAGGCGCAATTTTTACATCT

Basic information

species Zea mays
transcript GRMZM2G130440_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130440_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os09g26880.4 (Oryza sativa), 3'ss of exon 6
tctgttcaacatactcaccagttctgttttagtggcaataaacttgctcagtaccgcagggaggctgttactttgtctaatgttgttgc--gattcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGTGGCTAGTGTATTGGAGAAGAACAACTTGCCAGGCGCAATTTTTACATCT
    || |||      |       | | |   | ||| |   |||||     || |    |   ||||   ||| |   |  |  || |   |   || |||||||||||||||||| |||||  ||||||||||||||||||| |||||||| || ||||||||||||| |||||||||||||||| ||||||||||| | 
-tcattaaactggtgaaggtccattatatctattgcattttccttgcatga-actgtcttggaactgtcctttttttgtaactaatttctaaacaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGTTGCCAGTGTATTGGAGAGGAACAACTTGCCAGGCTCAATTTTTACAGCA

upper sequence: GRMZM2G130440_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 7
tctgttcaacatactcaccagttctgttttagtggcaataaacttgctcagt---accgcaggg---aggctgttactttgtctaatgttgttgcgattcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGTGGCTAGTGTATTGGAGAAGAACAACTTGCCAGGCGCAATTTTTACATCT
  |||||    ||  |     || | | | ||  | || |  |||| |   |   |   || |    | |||   |  |       |    |  |     ||| ||||| ||||||||||||||||||||  |||| |||||  |||||||  ||||||||   ||  | ||||| |||||||||||||| ||||| || || |||
-ttgttctctttatcc-----ttttctataagaaggaagactcttgtttccttgaattacatgttttatgctagaaaatgactacttaccataacctacattatagGAAGGGTGCTCCAACAACTCCACTAGTCACCATTGCCGTGACAAAGCTAGTGGCTGAAGTTCTTGAGAAAAACAACTTGCCAGGTGCAATATTCACCTCT
















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|149097409|gb|EE183263.2|EE183263
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|149070632|gb|EE159042.2|EE159042
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|211519447|gb|FK985265.1|FK985265
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|149008575|gb|EE040753.2|EE040753
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|78081606|gb|DV510018.1|DV510018
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|67033024|gb|CO461773.1|CO461773
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCNCA-CAACTCCACTGATCACTATTGCAATGACAAAAATAG
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTC-CAACAACTCCACTGATCACTATTGCAATGACAAAAATAG
EST: gi|149108383|gb|EE292721.2|EE292721
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|211385951|gb|FK985193.1|FK985193
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAG-TGCTCCCACAACTCCACTG
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTG
EST: gi|149076636|gb|EE165275.2|EE165275
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|13126736|gb|BG317306.1|BG317306
EST:     GTTGGAATGCTTGTATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|18659627|gb|BM500437.1|BM500437
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|149110789|gb|EE190608.2|EE190608
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|148963296|gb|EE014287.2|EE014287
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|211396477|gb|FK985252.1|FK985252
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAG-TGCTCCA-CAACTCCACTGAT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGAT
EST: gi|149073717|gb|EE162025.2|EE162025
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|71767769|gb|DR965706.1|DR965706
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|67042959|gb|CO469214.1|CO469214
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|149021323|gb|EE045783.2|EE045783
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|60398824|gb|DN231640.1|DN231640
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|211380674|gb|FK985159.1|FK985159
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGNAATTTGTGTCGTCTG                         GAAAGGT-CTCC
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATT-GTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCC
EST: gi|148982784|gb|EE028613.2|EE028613
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|211269838|gb|FK985131.1|FK985131
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAAATGTGTCGTCTG                         GAAAG-TGCTC
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTC
EST: gi|13126340|gb|BG316910.1|BG316910
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|148935117|gb|EC879157.2|EC879157
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|149059483|gb|EE156967.2|EE156967
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|148962667|gb|EE013566.2|EE013566
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|60358490|gb|DN225463.1|DN225463
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|149082793|gb|EE172015.2|EE172015
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
EST: gi|211267389|gb|FK985108.1|FK985108
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCCACAACTCCACTGATCACTATTGCCATGA
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGA
EST: gi|211380667|gb|FK985152.1|FK985152
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGTAATTGTGTCGTCTG                         GAAAGGTGCTCCA-CAACTCCACTGA
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGA
EST: gi|148935242|gb|EC879279.2|EC879279
EST:     GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG                         GAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT
genomic: GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGT

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), 46 (downstream exon)
Score: 368

GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGTGGCTAGTGTATTGGAGAAGAACAACTTGCCAGGCGCAATTTTTACATCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 722

GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGTGGCTAGTGTATTGGAGAAGAACAACTTGCCAGGCGCAATTTTTACATCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 422

GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGTGGCTAGTGTATTGGAGAAGAACAACTTGCCAGGCGCAATTTTTACATCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 383

GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatgg ... attcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGTGGCTAGTGTATTGGAGAAGAACAACTTGCCAGGCGCAATTTTTACATCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcagtaccgcagggaggctgttactttgtctaatgttgttgcgattcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGTGGCTAGTGTATTGGAGAAGAACAACTTGCCAGGCGCAATTTTTACATCT
                             gtctaat  putative branch site (score: 383)
                                              ttcttac  putative PPT
                      ttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgttcaacatactcaccagttctgttttagtggcaataaacttgctcagtaccgcagggaggctgttactttgtctaatgttgttgcgattcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGTGGCTAGTGTATTGGAGAAGAACAACTTGCCAGGCGCAATTTTTACATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - caacata
- - - - - - - -caccagt
- - - - - - - - - - - tctgttt
- - - - - - - - - - - - - - - - - -caataaa
- - - - - - - - - - - - - - - - - - - - - cttgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt