Sequence
atgc intronic sequence ATGC exonic sequence...ttctataggattttaatccttcaaagttcctccattttttctttgttccaaaggagcccttaaaatgcattcacatcatattgttgtttgattgatgtagGTTGACACCACCATACTTGGCCTTGATGACGTGAGGGCAAAGGAAATGCCTTATATTGCTAGCATGGGTATCTATGTTTTCAGCAAAGATGTAATGCTTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 3
-----------------ttctataggattttaatccttcaaagttcctccattttttctttgttccaaaggagcccttaaaatgcattcacatcatattgt-tgtttgattgatgtagGTTGACACCACCATACTTGGCCTTGATGACGTGAGGGCAAAGGAAATGCCTTATATTGCTAGCATGGGTATCTATGTTTTCAGCAAAGATGTAATGCTTC
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gtatgcaaatgacgtgcctttcttgctaacttgtgatatacagttgtgagatatcag--ttattacaccacatacttccatatcaaaactcattttgttgcctattttcgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCTTATATTGCTAGCATGGGTATCTATGTGATTAGTAAAAATGTAATGCTTC
upper sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 3
ttctataggattttaatccttcaaagttcctccattttttctttgttccaaaggagcccttaaaatgcattcacatcatattgttgtttgattgatgtagGTTGACACCACCATACTTGGCCTTGATGACGTGAGGGCAAAGGAAATGCCTTATATTGCTAGCATGGGTATCTATGTTTTCAGCAAAGATGTAATGCTTC
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------------gtaagcccatataa------catgtattatatgttgttattta--tctggaaattattacctgagcaattgcttaaaaatgccactagGTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAGGAATTGCCTTATATTGCTAGCATGGGTATATATGTTGTTAGCAAAAACGTGATGTTAG
upper sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 3
ttctataggattttaatccttcaaagttcctccattttttctttgttccaaaggagcccttaaa-atgcattcacatcatattgttgtttgattgatgtagGTTGACACCACCATACTTGGCCTTGATGACGTGAGGGCAAAGGAAATGCCTTATATTGCTAGCATGGGTATCTATGTTTTCAGCAAAGATGTAATGCTTC
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-----------gcaagcccatataagatgtattatatgttgttatttatctggaaattattacctgaacaattgcttaaaaatgccacttttcttttctagGTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAAGAAATGCCTTATATTGCTAGCATGGGTATATATGTTGTTAGCAAAAATGTGATGTTAG
upper sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 2
ttctataggattttaatccttcaaagttcctccattttttctttgttccaaaggagcccttaaaatgcattcacatcatattgttgtttgattgatgtagGTTGACACCACCATACTTGGCCTTGATGACGTGAGGGCAAAGGAAATGCCTTATATTGCTAGCATGGGTATCTATGTTTTCAGCAAAGATGTAATGCTTC
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---------------gtactataaactttacgctacttctctgcttcatcatgcggccttgtaaattaa--aaaatctcgat-ttctttgctc---ctagGTTGACACAACAATTCTAGGTCTTGATGATCAGAGAGCCAAGGAGATGCCTTTCATTGCTAGTATGGGTATTTATGTTGTAAGCAGAGATGTAATGCTAG
upper sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 3
----------------------ttctataggattttaatccttcaaagttcctccatttt----ttctttgttccaaaggagcccttaaaatgc--attcacatcatattgttgtttgattgatgta-gGTTGACACCACCATACTTGGCCTTGATGACGTGAGGGCAAAGGAAATGCCTTATATTGCTAGCATGGGTATCTATGTTTTCAGCAAAGATGTAATGCTTC
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gtagatgatatttgaaataaacattcgtattaattta-tgcttttgtgttcctctattctacaattttgtagttttaaagttggttaagaaggctgatacgttttcctttctgaactgttccttttaagGTCGATACTACCATCCTGGGTCTTGATGATGAGAGAGCTAAAGAAATGCCTTACATTGCTAGTATGGGTATATATGTCGTCAGCAAAGATGTGATGTTAGMapped 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|149015028|gb|EE044774.2|EE044774EST: TCTTTGAGTTTGCTGAGAAACCGAAAGGAGAGCAGTTGAAAGCAATGATG GTTGAC-CCACC
genomic: TCATTGAGTTTGCTGAGAAACCGAAAGGAGAGCAGTTGAAAGCAATGATGgtacacataa ... attgatgtagGTTGACACCACC
EST:
gi|67037455|gb|CO464271.1|CO464271EST: TCATTGAGTTTGCTGAGAAACCGAAAGGAGAGCAGTTGAAAGCAATGATG GTTGACACCACCATACTTGGCCTTGATGACGTGAGGGCAAAGGAAATGCCT
genomic: TCATTGAGTTTGCTGAGAAACCGAAAGGAGAGCAGTTGAAAGCAATGATGgtacacataa ... attgatgtagGTTGACACCACCATACTTGGCCTTGATGACGTGAGGGCAAAGGAAATGCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccaaaggagcccttaaaatgcattcacatcatattgttgtttgattgatgtagGTTGACACCACCATACTTGGCCTTGATGACGTGAGGGCAAAGGAAATGCCTTATATTGCTAGCATGGGTATCTATGTTTTCAGCAAAGATGTAATGCTTC
gattgat putative branch site (score: 4)
ttaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctataggattttaatccttcaaagttcctccattttttctttgttccaaaggagcccttaaaatgcattcacatcatattgttgtttgattgatgtagGTTGACACCACCATACTTGGCCTTGATGACGTGAGGGCAAAGGAAATGCCTTATATTGCTAGCATGGGTATCTATGTTTTCAGCAAAGATGTAATGCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG