Sequence
atgc intronic sequence ATGC exonic sequencegtctgcctcccttggatagctctttaacaattttcttggattttggtttaaatagatatcctgtataatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 29
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 46
---------gtctgcct-----cccttggatagctctttaacaattttctt----ggattttggtttaaatagatatcctgtataatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT
|| ||| | | ||||| || || |||||| || ||| | | || ||||| || || ||| ||||| || || ||||| |||||| | |||||||||||||| || |||||||||||||| |||||||| || || ||||| || ||||||||||| ||||||
gttactgctgttctcctggagcttaatagttagcttttaaatttatttcttttggggttttagatacaagtagatgctttgcatgtcctgcagGGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGAACTTGTAAAGCTTCGTGGTACAGCAATCAAAGGTCACCTTTCAATGGTT
upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 29
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 49
--gtctgcctcccttggatagctctttaacaattttcttggattttggtttaaa-------taga---------tatcctgta-taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT
| | || |||||||| | | ||| || ||| | |||| |||| ||| | || | | | |||||||||||||||||| || || ||| ||||||| ||||| || ||||||||||||| |||||||| || | |||||||||||||| ||||| ||||||
gtatataactttgttggatagagttactgcttcttttttttttttccttataaaataaaactagaaccactttttattttctaatgttgtatagGGCTGGTGCTGATGACAAACCTTTACGAATGGTAAAAACTGTTCTGCATGAACTTGTCAAGCTTCGTGGTGCAGCAATAAAGGGTCATCTTTCAATGGTT
upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 29
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 48
----gtctgcctcccttggatagctctttaacaattttctt-------ggattttggtttaaat-agatatcctgtataatct-------gtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT
| | || |||||||| | || | | || | | ||| | ||| | ||| | | |||||||||||||||||| || || ||| ||||||| ||||| || ||||||||||||| |||||||| || | |||||||||||||| ||||| ||||||
gtatatataactttgttggatagagttactactctcctttttttaaaaaaaaaaaaactcgaatcacttattttctattgttttatttgtatagGGCTGGTGCTGATGACAAACCTTTACGAATGGTAAAAACTGTACTGCATGAACTTGTCAAGCTTCGTGGTGCAGCAATAAAGGGTCATCTTTCAATGGTT
upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 29
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 18
---------------------------------------------------------------gtctgcctcccttggatagctctttaacaattttcttggattttggtttaaatagatatcctgtataatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT
|| | | ||| | |||| | ||||| |||| | | | || || | | | || ||||| |||||||| || |||||| | ||||| ||||| || | ||||||||||| |||||||| ||||| |||||||||||||||||||| ||||||
gtatcccttgtgtaatcaagttccgaaaaatttcaggatttttctttgttttttaggcaatgcagttgatttttatcattagttgcttaatgttcttctt-----ttggctgttaca-atgaaatgaactaccataagAGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGAACTTGTTAAGCTTCGCGGAACTGCAATAAAGGGTCACCTTTCTATGGTTMapped 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|18450668|gb|BM428946.1|BM428946EST: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
EST:
gi|87152573|gb|DY397362.1|DY397362EST: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
EST:
gi|67035401|gb|CO463934.1|CO463934EST: GCATCCATATTTATTTANCA-GAACTGGGAATGGAAGAAATACGGAGAAG GGCTGGTGCTGATGATAAGCCATTAAGAATGGGTCAAA-CCGTCTTGCATG
genomic: GCATCCATATTTATTTA-CAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGG-TCAAAACCGTCTTGCATG
EST:
gi|22489973|gb|BU049896.1|BU049896EST: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
EST:
gi|67019308|gb|CO448057.1|CO448057EST: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
EST:
gi|32851907|gb|CD991588.1|CD991588EST: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
EST:
gi|19822797|gb|BQ048821.1|BQ048821EST: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
EST:
gi|67011174|gb|CO439923.1|CO439923EST: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
EST:
gi|19822549|gb|BQ048573.1|BQ048573EST: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG GGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGA
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:
114GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT
Block sizes:
46 (upstream exon),
49 (downstream exon)
Score:
42GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT
Block sizes:
48 (upstream exon),
47 (downstream exon)
Score:
62GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT
Block sizes:
46 (upstream exon),
46 (downstream exon)
Score:
72GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcc ... taatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttaacaattttcttggattttggtttaaatagatatcctgtataatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT
ctttaac putative branch site (score: 72)
attttggtttaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgcctcccttggatagctctttaacaattttcttggattttggtttaaatagatatcctgtataatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC