Sequence
atgc intronic sequence ATGC exonic sequencegttcaatatgtttcatgcttgcaaaactctacttcttattctaatgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 3
gttcaatatgtttcatgcttgcaaaactctact-tcttattctaatgaactgctggcttatgatgg--tgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
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gtttgatatgctccatagttttgatctcaagctgttttgttttaatgtcctgaa----tatgatggcatatgttcttgtcctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGT
upper sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G26440.1 (Glycine max), 3'ss of exon 3
-------------gttcaatatgtttcatgcttgcaaaactctacttcttattctaatgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
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gtatacataatttcttgaatatttttgcagctttctgatgtttctgttttcttcatgtaaaata-----tgttgatgtgatttgtcatgccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT
upper sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G08710.1 (Glycine max), 3'ss of exon 3
gttcaatatgtttcatgcttgcaaaactctacttcttattcta--atgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
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--gtattagttttcatggcattcctattttatacctgatttcatcatgaaaagtatgtttatcat---atttatcacacaaattgtagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT
upper sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G08600.1 (Glycine max), 3'ss of exon 3
------------gttcaatatgtttcatgcttgcaaaactctacttcttattcta--atgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
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gtattgatatttcttggatgt-tttcatagccttcctattttatacctgatttcatcatgaaaaatatgtttatcat---atttatcacgcaaattgtagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT
upper sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 3
-------------gttcaatatgtttcatgcttgcaaaactctacttcttattctaatgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
|| ||||| ||| | || | || ||| | || ||| || | | ||||| ||| | | || || ||||| || ||| |||||||| || || | || |||||||| ||||||||||| ||||| || || | ||||||||||||||||| ||||| || |
gtatacatagtttcttgaatattttttcagttttctaatgtctctgttttcttcatatatata------tgttgatgtcatttgtcataccaattgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT
upper sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 3
gttcaatatgtttcatgcttgcaaaactctacttcttattctaatgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
||| ||| | | |||| |||| || || |||| | | || | || || | || || | || | ||| |||||||| | |||| || || |||||||||||||| || ||||| || || | ||||||||||||||||||||||||| ||
----gtaatggttcttccaaattggtctctctttctctctcccttgctctgcc--tctctaatcctaattggtctgatgcatatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGAT
upper sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
-----------gttcaa-tatg--tttcatgcttgcaaaactctacttcttattctaatgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
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gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatt--tattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCATMapped 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|18655221|gb|BM500026.1|BM500026EST: TTGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAG TCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAA
genomic: TCGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAGgttcaatatg ... catgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAA
EST:
gi|18963194|gb|BM660294.1|BM660294EST: TTGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAG TCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAA
genomic: TCGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAGgttcaatatg ... catgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAA
EST:
gi|42491897|gb|CK700943.1|CK700943EST: TCGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAG TCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAA
genomic: TCGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAGgttcaatatg ... catgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAA
EST:
gi|18662217|gb|BM501806.1|BM501806EST: TTGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAG TCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAA
genomic: TCGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAGgttcaatatg ... catgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAA
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:
76TTGTTGGAAACTGTTATTAAAAACTGTGGGGATATACTTCACATGCATGTCGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAGgttcaatatg ... catgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
Block sizes:
49 (upstream exon),
47 (downstream exon)
Score:
135TTGTTGGAAACTGTTATTAAAAACTGTGGGGATATACTTCACATGCATGTCGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAGgttcaatatg ... catgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
154TTGTTGGAAACTGTTATTAAAAACTGTGGGGATATACTTCACATGCATGTCGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAGgttcaatatg ... catgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
Block sizes:
49 (upstream exon),
47 (downstream exon)
Score:
105TTGTTGGAAACTGTTATTAAAAACTGTGGGGATATACTTCACATGCATGTCGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAGgttcaatatg ... catgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcttattctaatgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
ttctaat putative branch site (score: 105)
ttttgttttc putative PPT
tattctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcaatatgtttcatgcttgcaaaactctacttcttattctaatgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA