Sequence
atgc intronic sequence ATGC exonic sequence...atttgcatctaatttttgtcggtttgtacttaatgcttcggtttacctgtgtgattctgacttggtttctgatttgtttggattggattgggttggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG
Basic information
species | Glycine max |
transcript | GLYMA20G35970.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G24100.1 (Arabidopsis thaliana), 3'ss of exon 4
----atttgcatc-taatttttgtcggtttgtacttaatgcttcggtttacctgtgtgattctgacttggtttctgatttgtttggattggattgggttggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG
|||||| | | || | || ||| || || | || || | | | || | | | || | ||| ||| | | ||||||| ||||| ||||| ||||| || || || | || ||||| |||||||| || |||||||| || |||||||||||||||
acatatttgcttggtgatgcatatcagtt-atatttg-tactgtgg---aacaaagaaatgcaataattgcttattggttggttgttcttctcatttcttaacagGGCTGATATCTGGTCATTTGGTATAACAGCACTTGAATTGGCCCATGGTCATGCACCTTTCTCAAAATATCCTCCCATGAAG
upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G10730.1 (Arabidopsis thaliana), 3'ss of exon 5
atttgcatctaatttttgtcggtttgtacttaatgcttcggtttacctgtgtgattctgacttggtttctgatttgtttggattggattgggttgg--acagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG
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--ttttatgtcaaatgaaatgaaaaatctttagaaactgtttgcatcaaagaaatgcaataacagttattggttggtttgttcttctgtaccttccttacagGGCTGATATATGGTCTTTTGGAATAACGGCGCTGGAGTTGGCTCACGGTCATGCACCTTTCTCAAAATATCCCCCTATGAAG
upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S227_24V6.1 (Physcomitrella patens), 3'ss of exon 4
atttgcatctaatttttgtcggtttgtacttaatgcttcggtttacctgtgtgattctgacttggttt-ctgatttgtttggattggattgggt----tggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG
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----gcaatta-ctttgattcacatatacgacatttgactttctgcttgtacgagtctaaaaccctctgttgaccaggaataagcggtataagcattgtatgcagAGCTGACATCTGGTCCTTTGGGATAACTGCTTTGGAGCTTGCTCATGGTCATGCACCCTTCTCCAAGTATCCTCCCTTGAAG
upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S27_49V6.1 (Physcomitrella patens), 3'ss of exon 4
atttgcatctaatttttgtcggtttgtacttaatgcttcggtttacctgtgtgattctgacttggtttctgatttgtttggattg----gattgggttgg--acagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG
| | || || | | | | | | | | | || ||| || | || | | | || || || | ||| |||||| || || |||||||||||||||||||| ||||| | || |||||||| || || ||||| || |||||||| || |||
---aaaaaatggttctttttgagat-cgcaggagccgttagct-acttgt-tgtcttggattcgaaaagagggtttttataatcattaaagctccgttcattgcagGGCTGACATATGGTCGTTTGGGATTACTGCACTGGAGCTTGCACATGGTCATGCTCCATTCTCAAAATATCCTCCAATTAAG
upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ34917 (Selaginella moellendorffii), 3'ss of exon 4
atttgcatctaatttttgtcggtttgtacttaatgcttcggtttacctgtgtgattctgacttggtttctgatttgtttggattggattgg-gttggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG
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-------------------------gtaatgga-gcttcttttttcttcttc--ttcttgcc--gatgagaatttttctaagcgttgttgttgtcctgcagGGCTGATATCTGGTCCTTCGGGATCACTGCGTTGGAGTTGGCTCACGGGCATGCACCGTTTTCGAAATATCCTCCGATGAAGMapped 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|6567234|gb|AW234845.1|AW234845EST: GATAGCGCCGGAGGTGCTGCAACCTGGAACCGGTTACAATTTCAA GGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCA
genomic: GATAGCGCCGGAGGTGCTGCAACCTGGAACCGGTTACAATTTCAAgtcagttagt ... ggttggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCA
EST:
gi|10845866|gb|BF068902.1|BF068902EST: GATAGCGCCGGAGGTGCTGCAACCTGGAACCGGTTACAATTTCAA GGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCA
genomic: GATAGCGCCGGAGGTGCTGCAACCTGGAACCGGTTACAATTTCAAgtcagttagt ... ggttggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgtgtgattctgacttggtttctgatttgtttggattggattgggttggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG
atttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgcatctaatttttgtcggtttgtacttaatgcttcggtttacctgtgtgattctgacttggtttctgatttgtttggattggattgggttggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG
- -tgcatct
- - - - - - - - - - - - - - - - - gcttcgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg