Sequence
atgc intronic sequence ATGC exonic sequencegtactctttcctctcccttctacgcaaatagcttcttcttttctttctttttttgtcctttaaccgactgataatgttgaatttgaagAGCAATTGCATTTTGCAGAAGTGGAAATGATGAAGGAGAGGTTTGCTAAGCTGCTTCTGGGAGAGGACATGTCTGGAGGCGGAAAAGGGGTGTGTACTGC
Basic information
species | Glycine max |
transcript | GLYMA12G02620.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G38430.1 (Arabidopsis thaliana), 3'ss of exon 1
gtactctttcctctcccttctacgcaaatagcttcttcttttctttctttttttgtcctttaaccgactgataatgttgaatttgaagAGCAATTGC-ATT---TTGCAGAAGTGGAAATGATGAAGGAGAGGTTTGCTAAGCTGCTTCTGGGAGAGGACATGTCTGGAGGCGGAAAAGGGGTGTGTACTGC------------------
||| || ||| ||| |||| | | || | || || || ||||| || | ||| || ||||| | || |||||||||||||| ||||||||||| ||||| || || ||||||||||| || || |||||||| ||||| ||
---------------------gtataaa-agtttccaaatttgacctcttttgtaaacattgat-gaacactaggattcaatttcccttttgtttcctattgggtttcagAAATTGAGATGATGAAGGAGAGATTTGCTAAGCTACTTCTCGGGGAAGACATGTCTGGTGGAGGTAAAGGGGTTTGTACGGCGCTTGCTATCTCCAACGC
upper sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g03620.t01 (Vitis vinifera), 3'ss of exon 2
gtactctttcctctcccttctacgcaaatagcttcttcttttctttctttttttgtcctttaaccgactgataatgttgaatttgaa---gAGCAATTGCATTTTGCAGAAGTGGAAATGATGAAGGAGAGGTTTGCTAAGCTGCTTCTGGGAGAGGACATGTCTGGAGGCGGAAAAGGGGTGTGTACTGC------------------
|| || | ||| | | || | || | || | || || || || || | | | || | ||||| ||||| || |||||||||||||| ||||||||||| || || || || || ||||||||||| || |||||||| ||||||||
-------ttgggaaccacaatggaggcgtagtatggtagagatcttggtgggttttatttgag--gattggtacgttttcatatacatttgtgctcataatttttgtagAAGCTGAGATGATGAAGGAGAGATTTGCTAAGCTTCTACTTGGGGAAGATATGTCTGGAGGAGGGAAAGGGGTTTGTACTGCCCTTGCCATCTCAAACGC
upper sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S28_109V6.1 (Physcomitrella patens), 3'ss of exon 2
gtactctttcctctcccttctacgcaaatagcttcttcttttctttctttttttgtcctttaaccgactgataatgttgaatttgaagAGCAATTGCATTTTGCAGAAGTGGAAATGATGAAGGAGAGGTTTGCTAAGCTGCTTCTGGGAGAGGACATGTCTGGAGGCGGAAAAGGGGTGTGTACTGC------------------
| || | || | | | | || | | | | | |||| | || || ||| |||| |||| | ||| | |||| || | |||||||||| ||||||||||||| |||||| ||||| || || || ||||| |||||||| || |||||||| || || |||||
ggtctgctaccaagcgagcttcctaccgttgca-catttgaccagccattttatttcagttg--cgagtgat--tgttatttctgattactttttgc-ttctacagAAGTGGAGATGATGAAGGAGAAGTTTGCAAAGCTTCTGCTTGGGGAGGATATGTCTGGTGGGGGAAAAGGTGTTTGCACTGCGTTGGCTATATCGAACTC
upper sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S58_274V6.1 (Physcomitrella patens), 3'ss of exon 2
gtactctttcctctcccttctacgcaaatagcttcttcttttctttctttttttgtcctttaaccgactgataatgttgaatttgaagAGCAATTGCATTTT--------GCAGAAGTGGAAATGATGAAGGAGAGGTTTGCTAAGCTGCTTCTGGGAGAGGACATGTCTGGAGGCGGAAAAGGGGTGTGTACTGC------------------
| | ||| | | | || | | | | | | ||| | | |||| ||| || || | |||| | || ||||| ||||| |||||||||||||||||||| || || | || || || || ||||| || || || |||||||| || || ||
------------tgcattactattcgagtgcattttatgatgcat--atgtcgtgtacacggctagtgtgatgctgtaatatgtgttgcctgattgtgtcttctgttcttgcagAGGTGGAGATGATGAAGGAGAGGTTTGCAAAACTATTGCTTGGTGAAGATATGTCAGGTGGGGGCAAAGGGGTTTGCACAGCGTTGGCTATATCGAATGC
upper sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S7_228V6.1 (Physcomitrella patens), 3'ss of exon 2
gtactctttcctctcccttctacgcaaatagcttcttcttttctttctttttttgtcctttaaccgactgataatgttgaatttgaagAGCAATTGCATTTTGCAGAAGTGGAAATGATGAAGGAGAGGTTTGCTAAGCTGCTTCTGGGAGAGGACATGTCTGGAGGCGGAAAAGGGGTGTGTACTGC------------------
| | ||| ||| | | || | | ||||| || | | ||| || || | | || || | || | |||| ||||||||||||||||||| |||||| ||||| || || || ||||| ||||| || || || ||||| || | || ||
----gcaaccaagcgagctctcaatcaatggaattttttgccttccgtttttatgccggcaagtgccaggatcattttta--tctaattgcgtcttgcttctacagAGGTGGAAATGATGAAGGAGAAGTTTGCAAAGCTACTGCTTGGGGAGGATATGTCAGGTGGGGGCAAAGGTGTTTCCACAGCCTTAGCTATATCGAACTCMapped 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|209700670|gb|BW673027.1|BW673027EST: CGGCAAAGACGTCGTCGTTTGGGATCACAAGCGTGACCTCGATTTGTCGG AGCAATTGCATTTTGCAGAAGTGGAAATGATGAAGGAGAGGTTTGCTAAGC
genomic: CGGCAAAGACGTCGTCGTTTGGGATCACAAGCGTGACCTCGATTTGTCGGgtactctttc ... gaatttgaagAGCAATTGCATTTTGCAGAAGTGGAAATGATGAAGGAGAGGTTTGCTAAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttcttttctttctttttttgtcctttaaccgactgataatgttgaatttgaagAGCAATTGCATTTTGCAGAAGTGGAAATGATGAAGGAGAGGTTTGCTAAGCTGCTTCTGGGAGAGGACATGTCTGGAGGCGGAAAAGGGGTGTGTACTGC
gactgat putative branch site (score: 3)
ttttctttcttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactctttcctctcccttctacgcaaatagcttcttcttttctttctttttttgtcctttaaccgactgataatgttgaatttgaagAGCAATTGCATTTTGCAGAAGTGGAAATGATGAAGGAGAGGTTTGCTAAGCTGCTTCTGGGAGAGGACATGTCTGGAGGCGGAAAAGGGGTGTGTACTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG