Sequence
atgc intronic sequence ATGC exonic sequence...tggttgatatctttctgttcttagtttttaaattttttagttattcaacaagtacaataaaacattggaacaatatgtgatagtacgcttgtctaatcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG
Basic information
species | Glycine max |
transcript | GLYMA12G06980.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
tggttgatatctttctgttcttagtttttaaattttttagttattcaacaagtac---aataaaacattggaacaatatgtgatagtacgcttgtctaatcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG
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--gtaga-actcaacaatgttgcattgttgccttgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgttcttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 2
---tggttga-tatctttctgttcttagtttttaaattttttagttattcaacaagtacaataaaacattggaacaatatgtgatagtacgcttgtctaatcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG
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gtggggttgagcaaccattgaattctagggtctatgctatcatgctatgggtcttgtcttgcagacattttggatgtt----gactttgttcttttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG
upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 3
tggttgatatctttctgttcttagtttttaaattttttagttatt-caacaagtacaataaaacattggaacaatatgt-gatagtacgcttgtctaatcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG
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--ctaggtttgtggggctgagcaaacattgaaatctagggtccttgctatgggtcttgccttgcagacatgttggatgttgactttgttcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG
upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 2
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 3
tggttgatatctttctgttcttagtttttaaattttttagttattcaacaagtaca-ataaaacattggaacaatatgtgatagt-acgcttgtcta-atcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG
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-------------------gtttgcattgaaattcctatccgatacaatagtagtttatgcgcgatttgattaagtactgatgtttatatttttttttaccagGTGATTGTTGCTGATAACTATTTCACTGGTTCAAAGGACAACCTTAAGAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCACG
upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------tggttgatatctttctgttcttagtttttaaattttttagtt-attcaacaagtacaataaaacattggaacaatatgtgatagtacgcttgtctaatcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG
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gttagcatggttttttcatcttatccagtctcactttctgtgctgattactgaataggcgacaaaaatataaacc--ataatcatatgcagcagctgacttcatacatactgtatgataagaagatcgtgtttgataatagttttacttccttagGTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGMapped 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|213606684|gb|DB959073.1|DB959073EST: CAAAGCAACCTCCCATGCCATCTCCCTTGCGGTTTTCCAAGTTCTTTCAG GTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAA
genomic: CAAAGCAACCTCCCATGCCATCTCCCTTGCGGTTTTCCAAGTTCTTTCAGgtgaactctc ... gtctaatcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caacaagtacaataaaacattggaacaatatgtgatagtacgcttgtctaatcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG
cttgtct CT-rich tract
tacaataaaacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggttgatatctttctgttcttagtttttaaattttttagttattcaacaagtacaataaaacattggaacaatatgtgatagtacgcttgtctaatcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG
- - - - - ctttctg
- - - - - - - - - - - - - - - - - - - - - - - - caagtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaaa