Sequence
atgc intronic sequence ATGC exonic sequence...actgttttgaggcacagtcagatttttcttttgtttaaattgcattacattgaagtacttccccatgtttctatgactgctcacatgttgattgaaacagGAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 18
actgttttgaggcacagtcagatttttcttttgtttaaattgcatt-acattgaa-gtacttccccatgtttctatgactgctcacatgttgattgaaa--cagGAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
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----tttcttggattattaaggtatcactttgggtgaactaacttttatatttactgttattcacttgatttctgtaattgctcatgtgtttgctaaaaaacagGAACTGTTGTTGATTCAAAGATCTGCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAG
upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 19
-----------actgttttgaggcacagtca---gatttttcttttgtttaaattgcattacattgaagtacttccccatgtttctatgactgctcacatgttgattgaaa---cagGAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
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gtatgttgcacattcccaaaaagcttatctacagaaatgcatttttgaatcattctttggtttttaaaatgattatctaatgggctg-gaattttcatgttttaaattgtctttcagGGACTGTTGTTGATACCAAAATCTGCCATCCAACAGAATTTGATTTTTATCTCTGCAGCCATGCTGGCATCCAG
upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 10
-------------------actgttttgaggcacagtcagatttttcttttgtttaaattgcattacattgaagtacttccccatgtttctatgactgctcacatgttgattgaaacagGAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
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gtacaatgagtgttcctgaattgctcgtgtacacaaataaatgtgtcattttttttgtttaaaactgattgtctaattggactaacttttta-aataattttcatctgtttt----cagGGACTGTAGTTGATTCCAAAATCTGTCATCCAACAGAATTTGATTTTTATCTCTGTAGTCATGCTGGCATCCAG
upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 18
actgttttgaggcacagtcag-atttttcttttgtttaaattgcattacattgaagtacttccccatgtttctatga--ctgctcacatgttgattgaaa--cagGAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
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-----------gtatgatgactgttcctgaattgtttgtgtt-ctttttgttaaaaaatgattgtctaattaggttaaccttttaacaattttatctgttttcagGGACTGTTGTTGATTCCAAAATCTGTCATCCAACAGAATTTGATTTTTATCTGTGCAGTCATGCTGGCATCCAGMapped 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|91877156|gb|EB407113.1|EB407113EST: CAATCACAAAGACAGAAGTAGCATGGACAAGAGTGGAAATATTTTGCCAG GAACTGTTGTTG
genomic: CAATCACAAAGACAGAAGTAGCATGGACAAGAGTGGAAATATTTTGCCAGgtagtgtatc ... attgaaacagGAACTGTTGTTG
EST:
gi|211241581|gb|FL211915.1|FL211915EST: CAATCACAAAGACAGAAGTAGCATGGACAAGAGTGGAAATATTTTGCCAG GAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCT
genomic: CAATCACAAAGACAGAAGTAGCATGGACAAGAGTGGAAATATTTTGCCAGgtagtgtatc ... attgaaacagGAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCT
EST:
gi|9566493|gb|BE476002.1|BE476002EST: CAATCACAAAGACAGAAGTAGCATGGACAAGAGTGGAAATATTTTGCCAG GAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACC
genomic: CAATCACAAAGACAGAAGTAGCATGGACAAGAGTGGAAATATTTTGCCAGgtagtgtatc ... attgaaacagGAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACC
EST:
gi|20301316|gb|BQ164259.1|BQ164259EST: CAATCACAAAGACAGAAGTAGCATGGACAAGAGTGGAAATATTTTGCCAG GAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACC
genomic: CAATCACAAAGACAGAAGTAGCATGGACAAGAGTGGAAATATTTTGCCAGgtagtgtatc ... attgaaacagGAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACC
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:
704GTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACAGAAGTAGCATGGACAAGAGTGGAAATATTTTGCCAGgtagtgtatc ... attgaaacagGAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
154GTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACAGAAGTAGCATGGACAAGAGTGGAAATATTTTGCCAGgtagtgtatc ... attgaaacagGAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
73GTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACAGAAGTAGCATGGACAAGAGTGGAAATATTTTGCCAGgtagtgtatc ... attgaaacagGAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
142GTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACAGAAGTAGCATGGACAAGAGTGGAAATATTTTGCCAGgtagtgtatc ... attgaaacagGAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacattgaagtacttccccatgtttctatgactgctcacatgttgattgaaacagGAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
tttctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgttttgaggcacagtcagatttttcttttgtttaaattgcattacattgaagtacttccccatgtttctatgactgctcacatgttgattgaaacagGAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- tgttttg
- - - - - - - - - - - - - - ttttgtt
- - - - - - - - - - - - - - - - - - - -ttgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgactgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttg