Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatgtatcatatgctcctctttcttactatgctatgctatcaattccattcattggtgtgatcacgattctatttagAGCGTGCGCTTGTATGATGCGAGTGCCAATGTGTTGAGAGGAGAGTTTATGCACGCTGGCCCCGTCCTCGATTGCTGCTTCCACGACGATTCCTCCGGCT
Basic information
species | Glycine max |
transcript | GLYMA20G26960.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G26960.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g33580.2 (Oryza sativa), 3'ss of exon 1
------------------------------------gtatgtatgtatcatatgct--cctctttcttactatgctatgctatcaattccattcattggtgtgatcacgattctatttagAGCGTGCGCTTGTATGATGCGAGTGCCAATGTGTTGAGAGGAGAGTTTATGCACGCTGGCCCCGTCCTCGATTGCTGCTTCCACGACGATTCCTCCGGCT
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gtcagcgacgatgcgcgtccctctccgttccttgcggtcttggtggcccgtaagtaaaccctagcccccctttgatttggaagatctgaccggggtttggttccttgcgatctcttttagACGGTGCGCCTCTACGACGCCGACGCGAACGTGCTCAAGGGTGAGTTCGTACACGCCGGGGCCGTGCTCGACTGCTGCTTCCACGACGACTCCTCCGGGT
upper sequence: GLYMA20G26960.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G899300_T01 (Zea mays), 3'ss of exon 1
-----------------------------gtatgtatgtatcatatgctcctct--ttcttactatgctatgctatcaattccattca--ttggtgtgatcacgattctatttagAGCGTGCGCTTGTATGATGCGAGTGCCAATGTGTTGAGAGGAGAGTTTATGCACGCTGGCCCCGTCCTCGATTGCTGCTTCCACGACGATTCCTCCGGCT
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gtcagtggtggtcagccgcctcctcccccgctccccccattctcccgctcgttaaaccctagctgtctgaccccactgatctgacttggtttggtttggtttgggctttgc--agACGGTGCGGCTCTACGACGCCGACGCCAACGTGCTCAAGGGGGAGTTCATGCACCCCGGGGCCGTCCTCGACTGCTGCTTCCACGACGACTCCTCGGGCT
upper sequence: GLYMA20G26960.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G151598_T01 (Zea mays), 3'ss of exon 1
----------------------gtatgtatgtatcatatgctcctctttcttactatgctatgctatc-aattccattcat------tggtgtgatcacgatt---ctatttagAGCGTGCGCTTGTATGATGCGAGTGCCAATGTGTTGAGAGGAGAGTTTATGCACGCTGGCCCCGTCCTCGATTGCTGCTTCCACGACGATTCCTCCGGCT
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gtaagtggtggtcagccgcctcctctcccgctcccgccattcccccgctcgtaaaacccta-gctgtctgaccccactgatctgacctggtttgatttggtttgggcttcgcagACGGTGAGGCTTTACGACGCTGACGCCAACGTGCTCAAGAGGGAGTTCATGCACCCTGGGGCCATCCTCGACTGCTGCTTCCACGACGACTCCTCAGGCT
upper sequence: GLYMA20G26960.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0091g00710.t01 (Vitis vinifera), 3'ss of exon 1
gtatgtatgtatcatatgctcctctttcttactatgctatgctatcaa--ttccattcattggtgtgatca----cgattctatttagAGCGTGCGCTTGTATGATGCGAGTGCCAATGTGTTGAGAGGAGAGTTTATGCACGCTGGCCCCGTCCTCGATTGCTGCTTCCACGACGATTCCTCCGGCT
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gtatgt-cgcaaaacctagctctgtttctt-caatgcttggatctcgaagctcaattcgatgttgaggtttgtttcgatttt-tttagAGTGTTCGGTTGTACGATGCGAGTGCAAATGTGTTGCGAGGAGAGTTCATGCACGGAGGCCCTGTCTTGGATTGCTGCTTCCATGACGATTCCTCAGGGTMapped 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|192305486|gb|FG998298.1|FG998298EST: TTCGATTCTCCAACCACAGCGATCATCTTTTGGTGTCCTCATGGGACAAG AGCGTGCGCTTGTATGATGCGAGTGCCAATGTGTTGAGAGGAGAGTTTATG
genomic: TTCGATTCTCCAACCACAGCGATCATCTTTTGGTGTCCTCATGGGACAAGgtatgtatgt ... ttctatttagAGCGTGCGCTTGTATGATGCGAGTGCCAATGTGTTGAGAGGAGAGTTTATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttactatgctatgctatcaattccattcattggtgtgatcacgattctatttagAGCGTGCGCTTGTATGATGCGAGTGCCAATGTGTTGAGAGGAGAGTTTATGCACGCTGGCCCCGTCCTCGATTGCTGCTTCCACGACGATTCCTCCGGCT
ttcttac putative branch site (score: 2)
ttctattt putative PPT
attctattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatgtatcatatgctcctctttcttactatgctatgctatcaattccattcattggtgtgatcacgattctatttagAGCGTGCGCTTGTATGATGCGAGTGCCAATGTGTTGAGAGGAGAGTTTATGCACGCTGGCCCCGTCCTCGATTGCTGCTTCCACGACGATTCCTCCGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT