Sequence
atgc intronic sequence ATGC exonic sequence...ctaacagctgtcatcagtaatgtattgatgaatgcaataatactattgcttatagttgtaattttgataattaatttgtttgtttatttactatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCAAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTCATTTATGCTGATACG
Basic information
species | Glycine max |
transcript | GLYMA01G03530.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G03530.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 9
ctaacagctgtcatcagtaatgtattgatgaatgcaataatactat-tgcttatagttgtaattttgataattaatttgtttgtttatttactatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCAAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTCATTTATGCTGATACG
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-acatttttgagattccccaaaaaggatcacatgtcttttcagtgggtatcctcattcatgaggatgttattaaactttacaagttgtcatattcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGGACTATGGTAGCAGGAGGAGGTGCAAGTGTCATCTATGCAGATACG
upper sequence: GLYMA01G03530.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
-------------------ctaacagctgtcatcagtaa-----tgtattgatgaatgcaataat---actattgcttatagttgtaattttgataattaatttgtttgtttatttac-tatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCAAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTCATTTATGCTGATACG
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gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
upper sequence: GLYMA01G03530.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S7_156V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------ctaacagctgtcatcagtaatgtattg-atgaatgcaata---atactattgcttatagttgtaattttgataattaatttgtttgtttatttactatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCAAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTCATTTATGCTGATACG
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gtatgcggcactgctctgatagtttgaggcgggctctctggtactaccaaaaccatgccgcatgtacgagctccctgttcgtttgtttccagtt-tagggcttttaattgacatagctacatgtttga---ttgcagACCGGTGCCTCCTTGAAATTGACAATCTTGAACCCTGAAGGCCGAATCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGMapped 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|14989894|gb|BI315575.1|BI315575EST: GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAG ACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCAAAGGGCCGAATTTGG
genomic: GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAGgtgcacaaat ... ctatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCAAAGGGCCGAATTTGG
EST:
gi|193554210|gb|FK511295.1|FK511295EST: GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAG ACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCAAAGGGCCGAATTTGG
genomic: GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAGgtgcacaaat ... ctatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCAAAGGGCCGAATTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcttatagttgtaattttgataattaatttgtttgtttatttactatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCAAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTCATTTATGCTGATACG
aattaat putative branch site (score: 3)
taattttgataattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaacagctgtcatcagtaatgtattgatgaatgcaataatactattgcttatagttgtaattttgataattaatttgtttgtttatttactatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCAAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTCATTTATGCTGATACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - cagctgt
- - - - - - - - - - - - - - -gaatgca
- - - - - - - - - - - - - - - - - - - - - ctattgc