Sequence
atgc intronic sequence ATGC exonic sequence...tttactgtgttggatagttcaaatgtttcttttgtttgaaatcacattacattgttcctattatgaggaattgaaagctcatcttacaatttaaatgcagATTAATATTATTGATACTCCAGGTCACGTGGATTTCACCATTGAGGTTGAAAGGGCACTCCGTGTTCTTGATGGAGCTATACTTGTACTATGTAGTGTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G056393_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 1
---tttac-tgtgttggatagttcaaatgtttcttttgtttgaaatcacattacattgttcctattatgaggaattgaaagctcatcttacaatttaaatgcagATTAATATTATTGATACTCCAGGTCACGTGGATTTCACCATTGAGGTTGAAAGGGCACTCCGTGTTCTTGATGGAGCTATACTTGTACTATGTAGTGTTG
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aaaggtacatgtataatgctctttggatcagtcttggattgctttttaggtt---ttggtataagtatttgaaagtgaaacctcaagatacaatttta-tgcagGTTAATATCATCGATACTCCAGGTCATGTGGATTTCACTATTGAGGTTGAAAGAGCACTCCGTGTTCTTGATGGTGCTATACTTGTGCTATGTAGTGTTG
upper sequence: GRMZM2G056393_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------------------tttactgtgttggatagttca--aatgtttcttttgtttgaaatcacattacattgttcctattatgaggaa--ttgaaagctcatcttacaatttaaatgcagATTAATATTATTGATACTCCAGGTCACGTGGATTTCACCATTGAGGTTGAAAGGGCACTCCGTGTTCTTGATGGAGCTATACTTGTACTATGTAGTGTTG
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gtgaggagatagaaaaaaagatcttccttgtggattctgtgattctaatttcttctcagattcgtcaaaattggccttggttgtt-taattgtgtagtaatcctattgcattgagctttgaaatttgttgttatgattgttgt-cagGTTAATATAATTGATACTCCTGGTCACGTTGACTTCACCATTGAAGTGGAGAGGGCTTTACGTGTACTAGACGGTGCGATTCTAGTCCTATGCAGTGTGG
upper sequence: GRMZM2G056393_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 1
-----tttactgtgttggatagttcaaatgtttcttttgtttgaaatcacattacattgttcctattatgaggaattgaaagctcatcttacaatt--taaatgcagATTAATATTATTGATACTCCAGGTCACGTGGATTTCACCATTGAGGTTGAAAGGGCACTCCGTGTTCTTGATGGAGCTATACTTGTACTATGTAGTGTTG
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ttgcaccctttttgctagat-gtttatatatt-cttttggttg----cccatt-caaaagaaaaaaaaaaaaaagaagaaaaatcatccagaaattgttttttgcagGTTAACATAATTGACACTCCTGGTCATGTCGACTTCACCATTGAAGTTGAGAGGGCTTTGCGTGTCCTTGATGGTGCCATTCTTGTCCTTTGTAGTGTTG
upper sequence: GRMZM2G056393_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S20_94V6.1 (Physcomitrella patens), 3'ss of exon 1
------tttactgtgttggatagttcaaatgtttcttttgtttgaaatcacattacattgttcctattatgaggaattgaaagctcatcttacaatttaaatgcagATTAATATTATTGATACTCCAGGTCACGTGGATTTCACCATTGAGGTTGAAAGGGCACTCCGTGTTCTTGATGGAGCTATACTTGTACTATGTAGTGTTG
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ctcgcacgatccatgtta-atttctcacgtgcccatgccttttttcattgaatagcatagtccac----tgatcgactggt-gttctctgtatgctggtggaacagATCAATATTATTGACACGCCAGGTCACGTTGATTTTACCATTGAGGTTGAAAGGGCTCTTCGCGTGCTTGATGGAGCAGTACTTGTGCTTTGTAGTGTTG
upper sequence: GRMZM2G056393_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S100_33V6.1 (Physcomitrella patens), 3'ss of exon 1
tttactgtgttgg-atagttcaaatgtttcttt--tgtttgaaatcacattacattgttcctatt-atgaggaattgaaagctcatcttacaatttaaatgcagATTAATATTATTGATACTCCAGGTCACGTGGATTTCACCATTGAGGTTGAAAGGGCACTCCGTGTTCTTGATGGAGCTATACTTGTACTATGTAGTGTTG
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---gctggatccacgttactttaatttttctatgtttttcgcaattttgtca-gtaaccacaatccactgcctgatgattgttctgtatatcctggcgggacagATTAATATCATTGATACACCAGGCCATGTCGATTTTACTATTGAAGTTGAAAGGGCTCTTCGCGTGCTTGACGGAGCGGTACTCGTGCTTTGTAGTGTGGMapped 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|31353864|gb|CD438221.1|CD438221EST: GGATCACCATTCAGTCTGCTGCCACCTACTGCACCTGGAAGGATTACCAG ATTAATATTATTGATACTCCAGGTCACGTGGATTTCACCATTGAGGTTGAA
genomic: GGATCACCATTCAGTCTGCTGCCACCTACTGCACCTGGAAGGATTACCAGgtccgtttgt ... ttaaatgcagATTAATATTATTGATACTCCAGGTCACGTGGATTTCACCATTGAGGTTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attacattgttcctattatgaggaattgaaagctcatcttacaatttaaatgcagATTAATATTATTGATACTCCAGGTCACGTGGATTTCACCATTGAGGTTGAAAGGGCACTCCGTGTTCTTGATGGAGCTATACTTGTACTATGTAGTGTTG
atcttac putative branch site (score: 3)
atcttacaatttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttactgtgttggatagttcaaatgtttcttttgtttgaaatcacattacattgttcctattatgaggaattgaaagctcatcttacaatttaaatgcagATTAATATTATTGATACTCCAGGTCACGTGGATTTCACCATTGAGGTTGAAAGGGCACTCCGTGTTCTTGATGGAGCTATACTTGTACTATGTAGTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT