Sequence
atgc intronic sequence ATGC exonic sequencegtaagtattatttacaacatatgccttgttcattttcttactttgctagaatgtgaaatattgcaatatctttatcaaacaagcataataataattctgtcttgttttcacatggaaacagTGACTTGTATTCAATTCAATCCCGTTGATGAAAATTACTTCATCAGTGGTTCCATAGATGGCAAAGTTCGAATATGGGGGATACATGAAGAACGAGTTGT
Basic information
species | Glycine max |
transcript | GLYMA04G39290.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G39290.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g33630.1 (Oryza sativa), 3'ss of exon 2
gtaagt--attatttacaacatatgccttgttcattttcttactttgctagaatgtgaaatattgcaatatctttatcaaacaagcataataataattctgtcttgttttcacatggaaacagTGACTTGTATTCAATTCAATCCCGTTGATGAAAATTACTTCATCAGTGGTTCCATAGATGGCAAAGTTCGAATATGGGGGATACATGAAGAACGAGTTGT
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-aaagttaattgcccacaaaatattttttcctaattttt---ctttcctt--atgtagtagatt----caacttaatgatgttgacctgatattcttt---tcttgtc----------aacagTTACATGTGTTCAATTCAATCCAGTTGATGAAAGGTACTTCATCAGTGGCTCAATAGATGGCAAAGTTCGTGTTTGGGATGTTTCAGACAAGCGAGTAGT
upper sequence: GLYMA04G39290.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g34080.1 (Oryza sativa), 3'ss of exon 3
gtaagtattatttacaacatatgccttgttcattttcttactttgctagaat---gtgaaatattgcaatatctttatcaaacaagcataataataattctgtc--ttgttttcacatgga-aacagTGACTTGTATTCAATTCAATCCCGTTGATGAAAATTACTTCATCAGTGGTTCCATAGATGGCAAAGTTCGAATATGGGGGATACATGAAGAACGAGTTGT
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---------------------------gattatatccttattgcgatgaaagacagtcttataatgttatatgtactttgggctattgcattgactttttttttcattcctttgaaattgttaacagTGACATGTGTTCAATTCAATCCTATCGATGAAAGATACTTCATCAGTGGTTCAATAGATGGAAAAGTTCGTGTTTGGGATGCTTTGGATAAGAGAGTAGT
upper sequence: GLYMA04G39290.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0044g00880.t01 (Vitis vinifera), 3'ss of exon 2
---------gtaagtattatttacaacatatgccttgttca----ttttcttactttgctagaat---gtgaaatattgcaata--tctttatcaaacaagcataataataattctgtcttgttttcacatggaaacagTGACTTGTATTCAATTCAATCCCGTTGATGAAAATTACTTCATCAGTGGTTCCATAGATGGCAAAGTTCGAATATGGGGGATACATGAAGAACGAGTTGT
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gtaagtataataagattcaaatgttacatcttcctatttcagtatttttcgtacttgtttttgttttcatgactatttgaaatggttccttatgtgaagactggaata-taatttggtttcctttttggatgtaaccagTGACATGCATTCAGTTCAATCCTGTTGATGACAATTATTTCATAAGCGGTTCCATAGATGGAAAAGTTCGAATTTGGGGAGTGTCAGAGAGGCGAGTTGTMapped 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|193487610|gb|FK449721.1|FK449721EST: CAATGTCTAAGTGTTTTCTATCACAAAGACTATG TGACTTGTATTCAATTCAATCCCGTTGATGAAAATTACTTCATCAGTGGTT
genomic: CAATGTCTAAGTGTTTTCTATCACAAAGACTATGgtaagtatta ... atggaaacagTGACTTGTATTCAATTCAATCCCGTTGATGAAAATTACTTCATCAGTGGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatctttatcaaacaagcataataataattctgtcttgttttcacatggaaacagTGACTTGTATTCAATTCAATCCCGTTGATGAAAATTACTTCATCAGTGGTTCCATAGATGGCAAAGTTCGAATATGGGGGATACATGAAGAACGAGTTGT
aagcataataataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtattatttacaacatatgccttgttcattttcttactttgctagaatgtgaaatattgcaatatctttatcaaacaagcataataataattctgtcttgttttcacatggaaacagTGACTTGTATTCAATTCAATCCCGTTGATGAAAATTACTTCATCAGTGGTTCCATAGATGGCAAAGTTCGAATATGGGGGATACATGAAGAACGAGTTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC