Sequence
atgc intronic sequence ATGC exonic sequencegtatgctatgcatgcacacatgttaatgtgattgatgctgcaatctttgcttcggtagaagaaccccgtttggttggttgaccctcgcgcttcttggcaatgcggcgcagCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCAGAGACGGTGAAGCTCATCCTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G086614_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g21140.1 (Oryza sativa), 3'ss of exon 2
gtatgctatgcatgcacacatgttaatgtgattgatgctgcaatctttgcttcggtagaagaaccccgtttggttggttgaccctcgcgcttcttggcaatgcggc------gcagCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCAGAGACGGTGAAGCTCATCCTG
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---------gtataatgcgatgttgcaatgat-gtttcttctttcatggcggactcggtagaacgcgatctgattggc--atgtttgctgttcttggcaatgcgcccgcgctgcagCATCTACGGTCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCTGAGACGGTGAAGCTGATCTTG
upper sequence: GRMZM2G086614_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
gtatgctatgcatgcacacatgttaatg-tgattgatgctgcaatctttgcttcggtagaagaaccccgtttggttgg---ttgaccctcgcgcttcttggcaatgcggcgc-----agCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCAGAGACGGTGAAGCTCATCCTG
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gtatataatgcg-----atgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattggcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG
upper sequence: GRMZM2G086614_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3
gtatgctatgcatgcacacatgttaatgtgattgatgctgcaatctttgcttcggtagaagaaccccgtttggttggttgaccctcgcgcttcttggcaatgcggcgcagCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCAGAGACGGTGAAGCTCATCCTG
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----gttattattgtttaggt-ttaactttgttaa--ctggggtcagtgtgc--atagttggtcaatggcagaaatattaacttatagtttttatttctgt-tgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
upper sequence: GRMZM2G086614_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G63450.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgctatgcatgcacacatgttaatgtgattgatgctgcaatctttgcttcggtagaagaaccccgtttggttggttgaccctcgcgcttcttggcaatg-cggcgcagCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCAGAGACGGTGAAGCTCATCCTG
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-------------------------------------gtattactcttgtttgga---acccattcattcttcttgttggatgttgtctacttaaagcaatggtggtgcagTACGTTTGGGCCAGTTCAGGACGTGAGGATACCTTACCAGCAGAAGAGGATGTTTGGGTTCGTGACCTTCATGTACCCAGAGACTGTGAAGAGCATTCTG
upper sequence: GRMZM2G086614_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
gtatgctatgcatgcacacatgttaatgtgattgatgctgcaatct--ttgcttcggtagaag--aaccccgtttggttggttgaccctcgcgcttcttggcaatgcggc-gcagCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCAGAGACGGTGAAGCTCATCCTG
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----gttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaattgtgggaagttgagagctttcggttggttt-ctaaatcgctgttttgttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
upper sequence: GRMZM2G086614_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
gtatgctatgcatgcacacatgttaatgtgattgatgctgcaatctttgcttcg-gtagaagaaccccgtttggttggttgaccctcgcgcttcttggcaatgcggcgcagCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCAGAGACGGTGAAGCTCATCCTG
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-------gtaattgc-tacgtgttggt-tggaaatttcttcaatttggggttcgtgttgtgaaatttagttaacctagttggcttgtgtgctttt------------gaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTAMapped 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|89247427|gb|DY619213.1|DY619213EST: TTCCCGGCCGACAGCACGTTCCGCGAGGAGGACGTCTCCAACTACTTCAG CATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCAT
genomic: TTCCCGGCCGACAGCACGTTCCGCGAGGAGGACGTCTCCAACTACTTCAGgtatgctatg ... tgcggcgcagCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCAT
EST:
gi|149101000|gb|EE187097.2|EE187097EST: TTCCCGGCCGACAGCACGTTCCGCGAGGAGGACGTCTCCAACTACTTCAG CATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCAT
genomic: TTCCCGGCCGACAGCACGTTCCGCGAGGAGGACGTCTCCAACTACTTCAGgtatgctatg ... tgcggcgcagCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagaagaaccccgtttggttggttgaccctcgcgcttcttggcaatgcggcgcagCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCAGAGACGGTGAAGCTCATCCTG
ggttgac putative branch site (score: 4)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctatgcatgcacacatgttaatgtgattgatgctgcaatctttgcttcggtagaagaaccccgtttggttggttgaccctcgcgcttcttggcaatgcggcgcagCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCAGAGACGGTGAAGCTCATCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA