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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatctagggatatatcatctatgcaattcttacctagcctttcagacactgtctcactaactatcttcacaatgttgatcaccaaatgaacttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTG

Basic information

species Zea mays
transcript GRMZM2G153393_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153393_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g08550.1 (Oryza sativa), 3'ss of exon 13
ctatctagggatatatcatctatgcaattcttacctagcctttcagaca--ctgtctcactaactatcttcacaatgttgatcacc---aaatgaacttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTG
     | |  |       | ||||  | |  |  |   ||||| | |||   ||  ||||||   ||  |   ||||||  ||||    |||  ||  | || |||||||  |||| ||||| || | |||||||||||| ||||||||||| ||||||||||| || ||||| |||||||||||||||||||| |||||||| |
-----ttgaaaagagaagtttatggcaatgatgtcacaccttttatacatcttgattcactagtgattgtattaatgttcgtcacggaaaaaaaaaactatgcagGCAGCGCAACAGAGTGCTGGGTGCACTGCCCCAGAGGTGGACATGACTGGTCAGTACACACTGAAGAGCGATGTCTACAGCTTTGGAGTAGTCATGCTAG

upper sequence: GRMZM2G153393_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA03G42360.1 (Glycine max), 3'ss of exon 15
ctatctagggatat--atcat---ctatgcaattcttacctagcctttcagacactgtctcactaactatcttcacaatgttgatc-accaaatgaacttgtgt--agGCAGCAGAACAAAGTG------CCGGATACACTGCCCCAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTG
      ||| ||||  |||||   ||   ||| |    | |  ||||| |  || || |||  |||      | | | | ||| || | |   ||  |     |  ||  |    | || | ||      | |||||   ||| || ||||| | | || | |||||||| ||  | || ||||||||||||||||||||||||||||      
------aggaatattgatcatgttcttaacaaatgcagcttttccttttacccagtgactc--taagccctataaaattattgttctaactcttggtcgcacattcagATATTGAACCATAATGTTGGATCTGGATATGATGCACCTGAAGTTGCCTTGTCTGGTCAGTATACTTTGAAAAGTGATGTCTACAGCTTTGGAGTTGTCA------
















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|40303178|gb|CK347565.1|CK347565
EST:     ACCTTTCAGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAG                         GCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT
genomic: ACCTTTCAGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAGgtaatggtca ... acttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT
EST: gi|149106214|gb|EE291907.2|EE291907
EST:     ACCTTTCAGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAG                         GCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT
genomic: ACCTTTCAGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAGgtaatggtca ... acttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT
EST: gi|211334695|gb|FL296071.1|FL296071
EST:     AGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAG                         GCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT
genomic: AGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAGgtaatggtca ... acttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT
EST: gi|67014194|gb|CO442943.1|CO442943
EST:     ACCTTTCAGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAG                         GCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT
genomic: ACCTTTCAGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAGgtaatggtca ... acttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT
EST: gi|211334696|gb|FL296072.1|FL296072
EST:     ACCTTTCAGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAG                         GCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGATATGACCGGT
genomic: ACCTTTCAGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAGgtaatggtca ... acttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT
EST: gi|60395662|gb|DN228532.1|DN228532
EST:     AAGCTTTTATTCCTGATGCTGAATTCCAG                         GCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT
genomic: AAGC-TTTATTCCTGATGCTGAATTCCAGgtaatggtca ... acttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT
EST: gi|211334693|gb|FL296069.1|FL296069
EST:     ACCTTTCAGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAG                         GCAGCAGAACAGAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT
genomic: ACCTTTCAGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAGgtaatggtca ... acttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT
EST: gi|111145781|gb|EE258166.1|EE258166
EST:     CTTTCAGATGCTGGACTTGCCAAGCCTTTATTCCTGAAGCTGAATTCCNG                         GCAGCAGAACAAA
genomic: CTTTCAGATGCTGGACTTGC-AAGC-TTTATTCCTGATGCTGAATTCCAGgtaatggtca ... acttgtgtagGCAGCAGAACAAA
EST: gi|101390185|gb|EB817025.1|EB817025
EST:     AGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATACC-G                         GCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT
genomic: AGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAGgtaatggtca ... acttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGT

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: 48 (upstream exon), 49 (downstream exon)
Score: 154

TAAGAATTTCAAGTCGTCAAACATTTTGCTGGACTCAGAATTCAATCCACACCTTTCAGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAGgtaatggtca ... acttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

TAAGAATTTCAAGTCGTCAAACATTTTGCTGGACTCAGAATTCAATCCACACCTTTCAGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAGgtaatggtca ... acttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

TAAGAATTTCAAGTCGTCAAACATTTTGCTGGACTCAGAATTCAATCCACACCTTTCAGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAGgtaatggtca ... acttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 115

TAAGAATTTCAAGTCGTCAAACATTTTGCTGGACTCAGAATTCAATCCACACCTTTCAGATGCTGGACTTGCAAGCTTTATTCCTGATGCTGAATTCCAGgtaatggtca ... acttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacactgtctcactaactatcttcacaatgttgatcaccaaatgaacttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTG
             taactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatctagggatatatcatctatgcaattcttacctagcctttcagacactgtctcactaactatcttcacaatgttgatcaccaaatgaacttgtgtagGCAGCAGAACAAAGTGCCGGATACACTGCCCCAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - -ctatgca
- - - - - - - - - - - - - - - - - - - - - -cagacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccaaa