Sequence
atgc intronic sequence ATGC exonic sequencegtcagttttctttttcattttcccttgtttgatgattccataaatattttttggtttgttactataatattgtcaagagtctcaatatttgatattcttgaacagGAGCAGAAACCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG
Basic information
species | Glycine max |
transcript | GLYMA13G42800.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 13
------------------gtcagttttcttttt---cattttccctt---gtttgatgattccataaatattttttggtttg--ttactataat----attgtcaagagtctca--atatttgatattcttgaacagGAGCAGAAACCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG
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gtatatgactattttctctttagacttaatagtgactattttctctttagacttaatagtttcagccacattcatggactaggactggtccagttctcattgtcccttttctcatcacattagctcatatgaaacagGTGGAGAAAATCCGGGAGTTGATGCTAATGGAAATTCTTACGATCTTTCAACAAAGTTGCTCCATCTTGCATGGCACCCAACTGAGAATTCCATCGCGTG
upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 13
gtcagttttctttttcattttcccttgtttgatgattccataaatattttttggtttgttactataatattgtcaagagtctcaatatttgatattcttga-acagGAGCAGAAACCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG
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--------------------gttagtggtcatagtacctgtaaaacttattcaagcttttactac--tctcttctggagtaaaaaacttt--tgttttggacgcagGATCAGAGAGTCCCGGAACAGAGGCAAATGGGAACGCCTACGATTTCACAACAAAGTTGCTGCATATGGCTTGGCACCCAACAGAGAACTCAATTGCTTG
upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 15
gtcagttttctttttcattttcccttgtttgatgattccataaatattttttggtttgttactataatattgtcaagagtctcaatatttgatattcttgaacagGAGCAGAAACCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG
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-------------gtcggtatctctctctctatcatctcgc---tcgtttaagcattattaaaaaattggcatgaatagaataaatactgaaatttgtaaaacagGATCAGAGAGTCCGGGAGTCGATGGGAATACTAATGCTCTTGATTACACAACAAAGCTGCTGCATCTTGCTTGGCATCCAAACGAGAACTCAATTGCTTG
upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 13
gtcagt--tttctttttcattttccct-tgtttgatgattccataaatatttt---ttggtttgttactataatattgtcaagagtctcaa---tatttgatattcttga---------acagGAGCAGAAACCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG
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gtgagtcttttcttgttctcttgctttctctctattcaaaccacaaatttttaaaatcgtcttttaagcaatattttcccccatttctcatatcctttttctattctggggaatccgtgacagGAGCCGATAGCCCAGGAGTTGATGCAAATGGAAATTCTTTTGATTTCACTACAAAGTTGCTACATCTAGCATGGCACCCAAGTGAAAACTCAATCGCCTGMapped 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|193623278|gb|FK577330.1|FK577330EST: AAGGCCTTCGAGATCACTGGGAAATAGTATAACACGTGTTGTAAGACGGG GAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAA
genomic: AAGGCCTTCGAGATCACTGGGAAATAGTATAACACGTGTTGTAAGACGGGgtcagttttc ... tcttgaacagGAGCAGAAACCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAA
EST:
gi|193561102|gb|FK520195.1|FK520195EST: AAGGCCTTCGAGATCACTGGGAAATAGTATAACACGTGTTGTAAGACGGG GAGCAGAAACCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAA
genomic: AAGGCCTTCGAGATCACTGGGAAATAGTATAACACGTGTTGTAAGACGGGgtcagttttc ... tcttgaacagGAGCAGAAACCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggtttgttactataatattgtcaagagtctcaatatttgatattcttgaacagGAGCAGAAACCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG
atttgat putative branch site (score: 5)
tattctt CT-rich tract
ttgttactataatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagttttctttttcattttcccttgtttgatgattccataaatattttttggtttgttactataatattgtcaagagtctcaatatttgatattcttgaacagGAGCAGAAACCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC