Sequence
atgc intronic sequence ATGC exonic sequencegtattgctgcatctgatttgctcatcttaagtttcttggttcttctcttctgtcaagtttttatttcctgcacaatatttttacatggaaaaaactcatgaatagaatttcgcccccttatttggtttaacttttctttctatgccttttacatgtagGTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTCAGAGATGCTTAGATGGAGGAAGGAATTTGGTGCTGACAATATAGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G157043_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g50616.1 (Oryza sativa), 3'ss of exon 2
gtattgctgcatctgatttgctcatcttaagtttcttggttcttctcttctgtcaagtttttatttcctgcacaatatttttacatggaaaaaactcatgaatagaatttcgc-ccccttatttggtttaacttttctttctatgccttt---------tacatgtagGTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTCAGAGATGCTTAGATGGAGGAAGGAATTTGGTGCTGACAATATAGAG
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---------------------------------gtgcaatttttttctgatctcagagtcacagttacttgg----atttctcctt-------actcctgcagaaaattcagcgttgcttatttgatttaaaatttcttcatgtgcctatgacatgttacacatgtagGTTCCTGAAAGCGCGAAAATTTGATATTGATAAAGCAAAACATATGTGGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAGAG
upper sequence: GRMZM2G157043_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G12260.1 (Glycine max), 3'ss of exon 2
gtattgctgcatctgatttgctcatcttaagtttcttggttcttctcttctgtcaagtttttatttcctgcacaatatttttacatggaaaaaactcatgaatagaatttcgcccccttatttggtttaacttttctttctatgccttttacatgtagGTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTCAGAGATGCTTAGATGGAGGAAGGAATTTGGTGCTGACAATATAGAG---
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--------------------------------------------------------gtgtgccttgcctttgataattttctttatt-------tcctgaaatggaatttttgcttctctttt---ttattttttatttttacatttt------atagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG
upper sequence: GRMZM2G157043_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G01260.1 (Glycine max), 3'ss of exon 2
gtattgctgcatctgatttgctcatcttaagtttcttggttcttctcttctgtcaagtttttatttcctgcacaatatttttacatggaaaaaactcatgaatagaatttcgcccccttatttggtttaacttttctttctatgccttttacatgtagGTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTCAGAGATGCTTAGATGGAGGAAGGAATTTGGTGCTGACAATATAGAG---
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-----------------------------------------------------aagaaataagaatggaaccccctattttcgtgtt-aaattacttatgatttttgga-cgaatgagcttatacctgaaatttcttaattatgtgattttta---agATTTTTGAAAGCGAGGAAGTTCGATATTGAAAAGGCAAAACATATGTGGACTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTATGCAG
upper sequence: GRMZM2G157043_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 2
gtattgctgcatctgatttgctcatcttaagtttcttggttcttctcttctgtcaagtttttatttcctgcacaatatttttacatggaaaaaactcatgaatagaatttcgcccccttatttggtttaacttttctttctatgccttttacatgta--gGTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTCAGAGATGCTTAGATGGAGGAAGGAATTTGGTGCTGACAATATAGAG---
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--------------------------------------------------------gtgtgccttgcccaaagtaattttcttcatt-------tcccgaaatggaatgtt------ttgcttaattt---tcttcttcttattttttttacttttacagGTTCCTGAAAGCAAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG
upper sequence: GRMZM2G157043_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 2
gtattgctgcatctgatttgctcatcttaagtttcttggttcttctcttctgtcaagtttttatttcctgcacaatatttttacatggaaaaaactcatgaatagaatttcgcccccttatttggtttaacttttctttctatgccttttacatgtagGTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTCAGAGATGCTTAGATGGAGGAAGGAATTTGGTGCTGACAATATAGAG---
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--------------------------------------------------tgaaaaaaattaagaatg-gaaccctattttggtgtt-atattacttatgattttggacgaatgaacttatac--ctggaatttcttaattattgatttta----aagATTTTTGAAAGCGAGGAAGTTTGATATTGAAAAGGCAAAGCATATGTGGACTGACATGCTACAATGGAGGAAGGAGTTTGGTGCTGATACTATTGTGCAG
upper sequence: GRMZM2G157043_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 3
gtattgctgcatctgatttgctcatcttaagtttcttggttcttctcttctgtcaagtttttatttcctgcacaatattt-ttacatggaaaaaactcatgaatagaatttcgcccccttatttggtttaacttttctttctatgcctt-ttacatgtagGTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTCAGAGATGCTTAGATGGAGGAAGGAATTTGGTGCTGACAATATAGAG---
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--------------------------------------------------------tattttatgttccaactattttttattatatggtattgcttca--actatgttttcataa--tgagtaggtataacattgttaagagcattatattacttgcagGTTCTTGAAAGCAAGGAAGTTTGATATTGAGAAAGCAAAGCACATGTGGACTGATATGATTCAGTGGAGGAAGGATTTTGGTGCTGACACAATTTTGGAGMapped 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|60356198|gb|DN223171.1|DN223171EST: GATGATGGTCTGTTGCCAGAACATCACGATGATTATCACACGATGTTGAG GTTCCTGAAAGCAAGAAAATTTAATATTGACAGAGCAAAACATATGTGGTC
genomic: GATGATGGTCTGTTGCCAGAACATCACGATGATTATCACACGATGTTGAGgtattgctgc ... ttacatgtagGTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTC
EST:
gi|42491822|gb|CK700868.1|CK700868EST: GATGATGGTCTGTTGCCAGAACATCACGATGATTATCACACGATGTTGAT GTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTC
genomic: GATGATGGTCTGTTGCCAGAACATCACGATGATTATCACACGATGTTGAGgtattgctgc ... ttacatgtagGTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaatttcgcccccttatttggtttaacttttctttctatgccttttacatgtagGTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTCAGAGATGCTTAGATGGAGGAAGGAATTTGGTGCTGACAATATAGAG
gtttaac putative branch site (score: 3)
cttttctttctatgcc CT-rich tract
tttaacttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgctgcatctgatttgctcatcttaagtttcttggttcttctcttctgtcaagtttttatttcctgcacaatatttttacatggaaaaaactcatgaatagaatttcgcccccttatttggtttaacttttctttctatgccttttacatgtagGTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTCAGAGATGCTTAGATGGAGGAAGGAATTTGGTGCTGACAATATAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA