Sequence
atgc intronic sequence ATGC exonic sequence...tttactttttacactgttggtgtatgaaaattaaatcattttctaatatattgaatttctttccaagaaaaataagcatgtcaactgtttgcatttgcagATGAGATGACATACGTGAATCTTCAACTGAATCCCGAAAGATATACTGGTTATACTGGTCCATCAGCAAGAAGGATATGGGATGCTGTCTACTCAGAGAA
Basic information
species | Glycine max |
transcript | GLYMA09G10830.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G521844_T01 (Zea mays), 3'ss of exon 3
tttactttttacactgttggtgtatgaaaattaaatcattttctaatatattgaatttctttccaagaaaaataagcatgtcaactgtttgcatttgcagATGAGATGACATACGTGAATCTTCAACTGAATCCCGAAAGATATACTGGTTATACTGGTCCATCAGCAAGAAGGATATGGGATGCTGTCTACTCAGAGAA
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gtaatttatctttgccttgatctattctattgcacattctttgtttcttgtttattatcattcttg--acgattatcaaattg-ttgtac-tgttttcagATGAGATGACTTACGTGAATCTTCAACTGAATCCTGAACGATACACTGGCTATACCGGTGATTCAGCAAGGAGGATATGGGATGCTATTTATAAAGAGAA
upper sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 3
tttactttttacactgttggtgtatgaaaattaaatcattttctaat--atattgaatttctttccaagaaaaataagcatgtcaactgtttgcatttgcagATGAGATGACATACGTGAATCTTCAACTGAATCCCGAAAGATATACTGGTTATACTGGTCCATCAGCAAGAAGGATATGGGATGCTGTCTACTCAGAGAA
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gtaatttatctttgccttgatcta-gtttattgca-cattctttgattcttatttatcatcattc--atgatgattatcaaattg-ctgtat-tgttttcagATGAGATGACTTACGTGAATCTTCAACTGAATCCTGAACGATACACTGGCTATACTGGTGATTCAGCAAGAAGAATATGGGACGCTATTTACAAAGAGAA
upper sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------tttactttttacactgttggtgtatgaaa--------attaaatcattttctaatatattgaatttctttccaagaaaaataagcat-gtcaactgtttgcat--ttgcagATGAGATGACATACGTGAATCTTCAACTGAATCCCGAAAGATATACTGGTTATACTGGTCCATCAGCAAGAAGGATATGGGATGCTGTCTACTCAGAGAA
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gtaacttttctttacagtctacttcatttttgattcttacatgtcgaaactctatcgctacttcatatataactggctcatgagatgatatgtaacaagtaggggtttta-gcatcgaattgctatgtgttagatgcagtttttgatgactgtatatatgatcgcagATGAAATGACATATGTTAATCTTCGGCTTAATCCTGAACGGTACACTGGCTATATTGGCCCATCAGCTAGAAGGATATGGGAAGCTATATACTCTGAGAA
upper sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 3
tttactttttacactg-ttggtgtatgaaaattaaatcattttctaatatattgaatttctttccaagaaaaataagcatgtcaactgtttg----catttgcagATGAGATGACATACGTGAATCTTCAACTGAATCCCGAAAGATATACTGGTTATACTGGTCCATCAGCAAGAAGGATATGGGATGCTGTCTACTCAGAGAA
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-----caatgacattgcttagtcaataacactccatgtttcttttcttttcttaagtttctttaatggtttaataaagcttttgatggttcattttcatttgcagCGGAGATGACATATGTGAATCTTCAACTGAACCCTGAACGCTACACTGGATATACTGGTCCATCTGCACGAAGGATATGGGATGCTATTTATACTGAGAAMapped 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|192326501|gb|FK018808.1|FK018808EST: ATGGACAGAAATAGACAATCCATGGACAAATGACGATGAGACTGACAATG ATGAGATGACATACGTGAATCTTCAACTGAATCCCGAAAGATATACTGGTT
genomic: ATGGACAGAAATAGACAATCCATGGACAAATGACGATGAGACTGACAATGgtgcgttact ... gcatttgcagATGAGATGACATACGTGAATCTTCAACTGAATCCCGAAAGATATACTGGTT
EST:
gi|209720049|gb|BW659448.1|BW659448EST: ATGGACAGAAATAGACAATCCATGGACAAATGACGATGAGACTGACAATG ATGAGATGACATACGTGAATCTTCAACTGAATCCCGAAAGATATACTGGTT
genomic: ATGGACAGAAATAGACAATCCATGGACAAATGACGATGAGACTGACAATGgtgcgttact ... gcatttgcagATGAGATGACATACGTGAATCTTCAACTGAATCCCGAAAGATATACTGGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatattgaatttctttccaagaaaaataagcatgtcaactgtttgcatttgcagATGAGATGACATACGTGAATCTTCAACTGAATCCCGAAAGATATACTGGTTATACTGGTCCATCAGCAAGAAGGATATGGGATGCTGTCTACTCAGAGAA
ttctaat putative branch site (score: 2)
aagaaaaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttactttttacactgttggtgtatgaaaattaaatcattttctaatatattgaatttctttccaagaaaaataagcatgtcaactgtttgcatttgcagATGAGATGACATACGTGAATCTTCAACTGAATCCCGAAAGATATACTGGTTATACTGGTCCATCAGCAAGAAGGATATGGGATGCTGTCTACTCAGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - -gttggtg
- - - - - - - - - - - - - -aaattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgtc