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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttgttgacgtatgctgaacattcacagcttcacgttacaacattaaaggaaactatgatggtcgatttgatgatttgttgtttcttcttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA

Basic information

species Zea mays
transcript GRMZM2G004932_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 1
--cttttgttgacgtatgctgaacattcacagcttcacgttacaacattaaaggaaactatgatggtcgatttgatgatttgttgtttc-ttcttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
        || || | ||||| |  |  |  | |||  |  |       |       | |||    | ||  |||||||||| | |||  ||| | |  |||||||||||| ||||||||||||||||||||||||||||||||||||||
atagccaattcac-tgtgctggat-tgaattgtttc-tggaaaggtgaaaccatggtccatgtgaattgagctgatgatttgctattttgttcatatgtgcagACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
















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|211119333|gb|FL065968.1|FL065968
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|71433707|gb|DR814757.1|DR814757
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|211119334|gb|FL065969.1|FL065969
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGANATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|211119336|gb|FL065971.1|FL065971
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|211119335|gb|FL065970.1|FL065970
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|211118534|gb|FL065953.1|FL065953
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|211118539|gb|FL065958.1|FL065958
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAGCAG
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAGCAG
EST: gi|211118536|gb|FL065955.1|FL065955
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|211119328|gb|FL065963.1|FL065963
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|211119329|gb|FL065964.1|FL065964
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|211119337|gb|FL065972.1|FL065972
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|211118531|gb|FL065950.1|FL065950
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|211118532|gb|FL065951.1|FL065951
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|211118537|gb|FL065956.1|FL065956
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|211119330|gb|FL065965.1|FL065965
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|211273595|gb|FL065975.1|FL065975
EST:     ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCG                         ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA

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: 233

CAGCCTCGCTGACGCCGCCTACGTCAAGATCTCCGAGGCCGACTTTGGATACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 225

CAGCCTCGCTGACGCCGCCTACGTCAAGATCTCCGAGGCCGACTTTGGATACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 295

CAGCCTCGCTGACGCCGCCTACGTCAAGATCTCCGAGGCCGACTTTGGATACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

CAGCCTCGCTGACGCCGCCTACGTCAAGATCTCCGAGGCCGACTTTGGATACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgc ... ttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaggaaactatgatggtcgatttgatgatttgttgtttcttcttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
                      atttgat  putative branch site (score: 110)
                               tttgttgtttcttctt  putative PPT
       aaactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttgttgacgtatgctgaacattcacagcttcacgttacaacattaaaggaaactatgatggtcgatttgatgatttgttgtttcttcttgttggcagACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- tttgttg
- - - - - - - tgctgaa
- - - - - - - - - - - - - -cagcttc
- - - - - - - - - - - - - - - - - - - tacaaca
- - - - - - - - - - - - - - - - - - - - - - - -aaaggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgatg