Sequence
atgc intronic sequence ATGC exonic sequence...gctggtaataaacaaagtgttatagtcaaaccatcaggtatttatataattttttaaaaattttacctgacactgttggggcaaatacatttatgtgcagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGAAAGTTCAGCAAACAGGAAGAGGAGACAAT
Basic information
species | Glycine max |
transcript | GLYMA10G38110.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G38110.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G25560.1 (Arabidopsis thaliana), 3'ss of exon 1
gctggtaataaacaaagtgttatagtcaaaccatcaggtatt--tatataattttttaaa---aattttacctgaca-ctgttggggcaaatacatttatgtgcagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGAAAGTTCAGCAAACAGGAAGAGGAGACAAT
|| | ||| | |||| | | || ||| | ||| | | ||| | ||||| | | | |||| ||| || ||||||||||| |||||||| |||||||| |||||||| || ||||| ||||| |||||||| | | | | || | | ||||| ||||| ||
----------------gtctctctttcatcttcttctttattagtttttagtttctcaaactgagtcaactttgataattgttgttgggatttaatttg---atagGGTTACAAAGGAATGGGAAGAGCTGCAGATTAAGATGGATTAATTACCTAAGACCAGGGTTAAAGAGGGATATGATTAGTGCAGAAGAAGAAGAGACTAT
upper sequence: GLYMA10G38110.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G48920.1 (Arabidopsis thaliana), 3'ss of exon 1
gctggta-ataaacaaagtgttatagtcaaaccatcaggtatttatataatttttta--aaaattttacctgacactgttggggcaaatacatttatgtgcagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGAAAGTTCAGCAAACAGGAAGAGGAGACAAT
|| || | | | || ||| | ||| || |||| | | ||||| | | |||| | | | |||| ||| ||||| |||||||| ||||| ||||||||||||||| |||| ||| |||| || ||| | |||| |||| ||||| || || | | |
agaaatatattttttcactttgttaaataaatatttaggctctttcgatatttgtcatcgggtttttatgtaaactaattggttttcacata---atgtatagGATTGCAGAGGAATGGGAAGAGTTGTAGATTAAGGTGGGTTAATTATTTAAGACCTGGACTTAAGAAGTCTTTATTCACTAAACAAGAGGAAACTATACT
upper sequence: GLYMA10G38110.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G52260.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------gctggtaataaacaaagtgttatagtcaaacc---atcaggtattta--tataattttttaaaaattttacctgac--actgttggggcaaatacatttatgtgc-agGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGAAAGTTCAGCAAACAGGAAGAGGAGACAAT
|| || || || | || | | || || ||| |||| | | | || | | | | || | | || | | ||| ||||| ||| |||||||||||||| || ||||| ||||||||||||||||| || ||||| |||||| ||||||| || ||| || || | ||||| ||||| ||
gtttttttttaatctctaaaatcttatattagactctctttttttcttaaccctatatcctatattagactcttaattctcatcattgttgttaatcttatccttaactaagagtaattgttgtgccagGATTGCAAAGGAATGGGAAAAGCTGCAGATTAAGGTGGATTAATTACCTAAGACCAGGACTAAAGAGGGGGTCGTTTAGTGAAGAAGAAGAAGAGACCAT
upper sequence: GLYMA10G38110.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g00050.t01 (Vitis vinifera), 3'ss of exon 1
-gctggtaataaacaaagtgttatagtcaaaccatcaggtatttatataattttttaaaaattttac-ctgacactgttggggcaaatacatttatgtgcagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGAAAGTTCAGCAAACAGGAAGAGGAGACAAT
| | || | |||| | | | || | | | || | | || | | || | | | || | | | | || |||||| ||||||||||||||||||||||| |||||||||||||||||||| |||| ||||||||||| | || | ||| | | |||| || ||||| ||
atgttcttttagtgccattgttgcatgttacataccatatgatcacatgttggtctagcattaatatgccttgattctttgaccttgtg-gtgcat-tgcagGTTTGCAAAGGAATGGAAAGAGCTGCAGATTAAGGTGGATTAACTACTTAAGACCAGGATTAAAACGCGGGATGTTTACGATCGAGGAGGAAGAGACGAT
upper sequence: GLYMA10G38110.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S189_29V6.1 (Physcomitrella patens), 3'ss of exon 1
------gctggtaataaacaaagtgttatagtcaaaccatcaggtatttatataattttttaaaaattttacctgacactgttggggcaaatacatttatgtgcagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGAAAGTTCAGCAAACAGGAAGAGGAGACAAT
| | |||| |||| | ||| | | | || | | | ||| || || | || | ||| | | | | | |||| || || || |||||| ||||| || ||||||||||| |||||||| ||||||| |||||| |||| ||| | || ||| | ||
tttcctctttgctctaaaaaaaga---aaagttcagatacc--ccgttgacaccaatttagaataagagt-tgtgtcgctgacgctggtgtgccctggaacaacagGGTTACAGAGATGTGGAAAAAGCTGCAGGTTAAGGTGGATAAACTATCTGAGGCCAGACTTAAAGCGAGGGGTTTTCTCACCAGCAGAGGAGAATCTGATMapped 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|192327064|gb|FK019281.1|FK019281EST: CATCCTTAAACATGGTCATGGCTGTTGGAGTTCCGTCCCCATTAAGGCAG GCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAA
genomic: CATCCTTAAACATGGTCATGGCTGTTGGAGTTCTGTCCCCATTAAGGCAGgttggtttct ... ttatgtgcagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataattttttaaaaattttacctgacactgttggggcaaatacatttatgtgcagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGAAAGTTCAGCAAACAGGAAGAGGAGACAAT
acctgac putative branch site (score: 3)
tttttaaaaattttac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gctggtaataaacaaagtgttatagtcaaaccatcaggtatttatataattttttaaaaattttacctgacactgttggggcaaatacatttatgtgcagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGAAAGTTCAGCAAACAGGAAGAGGAGACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
gctggta
- - - - -aaacaaa
- - - - - - - - - - - - -tcaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttggg