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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcatgttgtgcaaattggtcttgatgaaggctacagttagccgtttgactgtactacttcactgttcaataatattccatgttaatattttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG

Basic information

species Zea mays
transcript GRMZM2G175510_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175510_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 2
ctcatgttgtgcaaattggtcttgatgaa-ggctacagttagccgtttgactgtactacttcactgttc-aataatattccatgttaatattttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG
          | |||||  || |  |  | ||||    ||  | ||    || |  | |||| ||  ||   |   |   |||  |  | |||     ||||||||||||||| |||||||| || |||||||||||  | || ||| |||| |||||||| || ||||||||||
----------gtaaattaatccttttctatggctctttttctctgtgatgct-tgttgcttctctcctctggtttcagatcatcgttgtttttgtggtacagGCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAGATGCTTCTTGATGCTGGTGGAG

upper sequence: GRMZM2G175510_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 2
ctcatgttgtgcaaattggtcttgatgaaggctacagttagccgtttg--actgtactacttcactgttcaataatattccatgttaatattttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG
  |   |   |  | | |||  || |  |   |  || | | | | ||  | ||| || ||  |      |||  |   | || || | |  | ||| |||||||||||||||||| || || || || ||||||||  |||||||| |||| ||||| || || ||||||||||
-actgataaagttactaggttctgtttgaatatgtaggttggcatgtgcaattgtgctgctcaatgaactaatgttgcac-atttttacaaatgcttgacagGCTGTTGCTGACATAATACGTACTACCTTGGGTCCACGATCCATGTTGAAGATGCTACTTGATGCTGGTGGAG
















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|71438455|gb|DR819505.1|DR819505
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG                         GCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTG-AA
EST: gi|211175329|gb|FL101110.1|FL101110
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCTAACATCCAGGCGGCCAAG                         GCTGTTGCTGACATCATTCGCACCACATTGGGTCCCAGATCCATGCTGAAA
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
EST: gi|211175332|gb|FL101113.1|FL101113
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG                         GCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
EST: gi|211175327|gb|FL101108.1|FL101108
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCTAACATCTAGGCGGCCAAG                         GCTGTTGCTGACATCATTCGCACCACATTGGGTCCCAGATCCATGCTGAAA
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
EST: gi|71332448|gb|DR803183.1|DR803183
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG                         GCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
EST: gi|31354620|gb|CD438977.1|CD438977
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCTAACATCCAGGCGGCCAAG                         GCTGTTGCTGACATCATTCGCACCACATTGGGTCCCAGATCCATGCTGAAA
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
EST: gi|32798447|gb|CD950683.1|CD950683
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCTAACATCCAGGCGGCCAAG                         GCTGTTGCTGACAGCATTC
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTC
EST: gi|211175325|gb|FL101106.1|FL101106
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCTAACATCCAGGCGGCCAAG                         GCTGTTGCTGACATCATTCGCACCACATTGGGTCCCAGATCCATGCTGAAA
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
EST: gi|211175333|gb|FL101114.1|FL101114
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG                         GCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
EST: gi|71428865|gb|DR809915.1|DR809915
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG                         GCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
EST: gi|94478012|gb|EB706970.1|EB706970
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG                         GCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
EST: gi|71448421|gb|DR829471.1|DR829471
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG                         GCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
EST: gi|211175328|gb|FL101109.1|FL101109
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG                         GCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
EST: gi|30306946|gb|CD001619.1|CD001619
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG                         GCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
EST: gi|74244741|gb|DT652655.1|DT652655
EST:     AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG                         GCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA
genomic: AGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAA

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), 48 (downstream exon)
Score: 318

AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 176

AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 168

AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAGgtacggattc ... ttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgactgtactacttcactgttcaataatattccatgttaatattttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG
                                   tgttaat  putative branch site (score: 168)
                                         tattttcttc  CT-rich tract
                    ttcaataatattccat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcatgttgtgcaaattggtcttgatgaaggctacagttagccgtttgactgtactacttcactgttcaataatattccatgttaatattttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- -atgttgt
- - - - - - - - - - - tgatgaa
- - - - - - - - - - - - - - - gctacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtta