Sequence
atgc intronic sequence ATGC exonic sequencegcatgctttatttttcttacaatttctttcttcttaaattattaatataaatgaaataggcttcacatatttttagacagttctgaaataacaaaagatggacccgggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCGGTTTGCGGGGAAGAAAGTTTTGGAACAGGTTCTGACCACATTCGTG
Basic information
species | Glycine max |
transcript | GLYMA20G29230.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 15
gcatgctttatttttcttacaatttctttcttcttaaattattaatataaatgaaataggcttcacatatttttagacagttctgaaataacaaaagatggacccgggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCGGTTTGCGGGGAAGAAAGTTTTGGAACAGGTTCTGACCACATTCGTG
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gttcaccctttttagtcaacagat--gtattttctaggtttgcaac-cagataaaattaggaggataaactttttgaca------aagcaact-----tgtat----gttttagGTTCCCACTGGATGGAAATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTG
upper sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 15
-------------------gcatgctttatttttcttacaatttctttcttcttaaattattaatataaatgaa-ataggcttcacatatttttagacagttctgaaataacaaaagatggacccgggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCGGTTTGCGGGGAAGAAAGTTTTGGAACAGGTTCTGACCACATTCGTG
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gtgaagcccttctgtactaatttgtcgtgattaacatggaaaactgtcttgcttaaaatggaaaggtttatatccattgacatacttctctcctaacaaactatgtccttaacaatgactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG
upper sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ34621 (Selaginella moellendorffii), 3'ss of exon 14
gcatgctttatttttcttacaatttctttcttcttaaattattaatataaatgaaataggcttcacatatttttagacagttctgaaataacaaaagatggacccgggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCGGTTTGCGGGGAAGAAAGTTTTGGAACAGGTTCTGACCACATTCGTG
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--------------------------------------------------gtacgggacgctaccgactttatgagcaatggttcacacagcaaaatt---------gttgaagGTTCCAACTGGCTGGAAGTTTTTTGGCAATCTCATGGACGCGGGAAAACTGTCGATTTGCGGAGAGGAAAGTTTTGGAACGGGATCTGATCATATTCGTG
upper sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ32824 (Selaginella moellendorffii), 3'ss of exon 14
gcatgctttatttttcttacaatttctttcttcttaaattattaatataaatgaaataggcttcacatatttttagacagttctgaaataacaaaagatggacccgggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCGGTTTGCGGGGAAGAAAGTTTTGGAACAGGTTCTGACCACATTCGTG
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--------------------------------------------------gtacgggacgctaccgactttatgagcgatggctcacacagcaaaatt---------gttgaagGTTCCAACTGGCTGGAAGTTTTTTGGCAATCTCATGGACGCGGGAAAACTGTCGATTTGCGGAGAGGAAAGTTTTGGAACGGGATCTGATCATATTCGTGMapped 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|120529538|gb|EH257672.1|EH257672EST: GTGGTGCTTTGGACCGTGTTGCTGAAAAATTGGACCTCCCTTTCTTTGAG GTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTG
genomic: GTGGTGCTTTGGACCGTGTTGCTGAAAAATTGGACCTCCCTTTCTTTGAGgcatgcttta ... cgggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTG
EST:
gi|120529768|gb|EH257902.1|EH257902EST: GTGGTGCTTTGGACCGTGTTGCTGAAAAATTGGACCTCCCTTTCTTTGAG GTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTG
genomic: GTGGTGCTTTGGACCGTGTTGCTGAAAAATTGGACCTCCCTTTCTTTGAGgcatgcttta ... cgggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttcacatatttttagacagttctgaaataacaaaagatggacccgggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCGGTTTGCGGGGAAGAAAGTTTTGGAACAGGTTCTGACCACATTCGTG
aaataac putative branch site (score: 2)
aaataacaaaagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatgctttatttttcttacaatttctttcttcttaaattattaatataaatgaaataggcttcacatatttttagacagttctgaaataacaaaagatggacccgggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCGGTTTGCGGGGAAGAAAGTTTTGGAACAGGTTCTGACCACATTCGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA