Sequence
atgc intronic sequence ATGC exonic sequence...ttcttgagatttttacaactatttagtcaatgtgttaatgagcagctagcttctatctacataattgataattgatagcaactatattttgacttttcagGTTGGAATGTCAATTGATCCAAAACTTCTTGTTTCAAACTTCCCAGTCATTACGGGCACACTAGGACTCTTAATATGTGGCAAGACTATCTTGGTTTGTT
Basic information
species | Glycine max |
transcript | GLYMA09G39770.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G093643_T01 (Zea mays), 3'ss of exon 12
---ttcttgagatttttacaactatttagtcaatgtgttaatgagcagctagcttctatctacataattgataattgatagcaactatattttgacttttcagGTTGGAATGTCAATTGATCCAAAACTTCTTGTTTCAAACTTCCCAGTCATTACGGGCACACTAGGACTCTTAATATGTGGCAAGACTATCTTGGTTTGTT
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ctatccatttatcttttccaac-atctaggtatttttaccactttctttaggacgatgagaat-tccttgattagttcttaca-ttgaggtttggttttccagGTTGGAATGTCTATTGACCCAAAGCTGCTTCTGTCAAACTTCCCAGCGATCTCTGTGATATTGAGTCTCTTGATAATTGGAAAGACATTGTTAGTTACAT
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 15
lower sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 11
--ttcttgag-atttttacaactatttagtcaatgtgttaatgagcagctagcttctatctacataattgat--aattgatagcaactatattttgacttttcagGTTGGAATGTCAATTGATCCAAAACTTCTTGTTTCAAACTTCCCAGTCATTACGGGCACACTAGGACTCTTAATATGTGGCAAGACTATCTTGGTTTGTT-
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cctgcttaaatgctcttgtaagattctaat---tttgtttccagctcttaaagtacaatttatctcgttcatgaaactaatggga--cgagctgcataaaatcagGTGGGCATGTCCATTGATCCAAAACTTCTTCTCGCCAACTTCCCTCTCATAATGGGGACCTTAGGACTCTTATTAGTTGGCAAGACTATATTAGTG-GTGA
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 15
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 12
------------------------------------------------------------ttcttgagatttttacaactatttagtcaatgtgttaatgagcagctagcttctatctacataattgataattgatagcaactatattttgact--tttcagGTTGGAATGTCAATTGATCCAAAACTTCTTGTTTCAAACTTCCCAGTCATTACGGGCACACTAGGACTCTTAATATGTGGCAAGACTATCTTGGTTTGTT-
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gtaatatgagtttcctaataactttttccatagtttatcatttctgaaaagaatgaggaactatagatggaaaaggaaaccttttacttgtgttctagtaagatcctgatattgttgtcaactgtaagcaaac--taacaaaaagagttccattgatttcagGTTGGAATGTCAATTGATCCGAAATTACTTCTCTCCAACTTCCCTGTCATAGTGGGAACTTTGGGACTCTTGATAGTGGGCAAAACTATGTTAGTC-GTGA
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 10
--------ttcttgagatttttacaactatttagtcaatgtgttaatgagcagctagcttctatctacataattgataattgatagcaactatattttgacttttcagGTTGGAATGTCAATTGATCCAAAACTTCTTGTTTCAAACTTCCCAGTCATTACGGGCACACTAGGACTCTTAATATGTGGCAAGACTATCTTGGTTTGTT
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ggatattggttttcaatttggcaggctgatattaccactgtattactgaat------catgattcttgatactt--ctattaacggaaatctttttgtgggtttccagGTGGGAATGTCTATTGATCCAAAGCTTCTTATTTCAAACTTTCCAGTTATAATGGGGACATTAGGACTCTTAATTGGTGGCAAGGCTTTATTGGTTGCTTMapped 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|16996864|gb|BM086236.1|BM086236EST: CTGATATTGCTCCTTATCGTGGCCTTCTTTTGGGGCTCTTCTTTATGACG GTTGGAATGTCAATTGATCCAAAACTTCTTGTTTCAAACTTCCCAGTCATT
genomic: CTGATATTGCTCCTTATCGTGGCCTTCTTTTGGGGCTCTTCTTTATGACGgtaggtgctg ... gacttttcagGTTGGAATGTCAATTGATCCAAAACTTCTTGTTTCAAACTTCCCAGTCATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagcttctatctacataattgataattgatagcaactatattttgacttttcagGTTGGAATGTCAATTGATCCAAAACTTCTTGTTTCAAACTTCCCAGTCATTACGGGCACACTAGGACTCTTAATATGTGGCAAGACTATCTTGGTTTGTT
ttttgac putative branch site (score: 3)
cttttc CT-rich tract
ataattgataattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcttgagatttttacaactatttagtcaatgtgttaatgagcagctagcttctatctacataattgataattgatagcaactatattttgacttttcagGTTGGAATGTCAATTGATCCAAAACTTCTTGTTTCAAACTTCCCAGTCATTACGGGCACACTAGGACTCTTAATATGTGGCAAGACTATCTTGGTTTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - -caatgtg
- - - - - - - - - - - - - - - - - - - - -gcagcta