Sequence
atgc intronic sequence ATGC exonic sequence...ttttattagtgttgcctaaaactgttgcacaatctgcttaatgcttttcttgtgagtaatggtgttgtattgtctgagtttttattttttgatatttcagTGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
Basic information
species | Glycine max |
transcript | GLYMA10G37020.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G37020.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G76720.1 (Arabidopsis thaliana), 3'ss of exon 8
-ttttattagtgttgcctaaaactgt-tgcacaatctgcttaat---gcttttcttgtgagtaatg-gtgttgtat-tgtctgagt--ttttattttttgatatttcagTGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
| | ||| || | | || || | | || | || || || | | ||| || | | | | || || || || |||||||| |||||| ||||| | || ||| | || | ||| |||||||| | || |||||||||||||||||||||||||| ||| |||||||||
gtatgattcatgccgtatgaatctctatttactgtttgtaatatacagcgtaacagacaagttattcatcctaaacgtaattgggtaacgttggttcttgatattacagTGGAGAAGGGGTCCCAGATCTCTTGCTGTGGTTGGTTCAATGGGCTCAGAAAACAATGGTTGAGAAACTTACATATGTTGACGAAGTGCAG
upper sequence: GLYMA10G37020.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G21160.1 (Arabidopsis thaliana), 3'ss of exon 5
ttttattagtgttgcctaaaactgttgcacaatctgc----ttaatgcttttcttgtgagtaatggtgttgtattgtctgagtttttattttt------tgatatttcagTGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
| || ||| || | |||| | || | || | | | || || | | | || | | ||| | || |||||||||||||| ||||| ||||| ||| | ||| | | ||| |||||||| | || ||||| ||||| |||||||||||||| ||| ||||||||
-------------gtctgaaatgtttttgctatctccaaattttagtctaacatagaggtcaaccatgcta-actaactaattgattaatgttggatactgatatttcagTGGGGAAGGGATTCCAGATCTTTTACTGTTCTTGGTTCAATGGGCTCAGAAAACGATGGTGGAGAAACTTACATATGTTGACAAAGTGCAG
upper sequence: GLYMA10G37020.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G76810.1 (Arabidopsis thaliana), 3'ss of exon 5
ttttattagtgttgcctaaaactgttgcacaatctgcttaatgcttttcttgtgagtaatggtgttgtattgtctgagtttttattttttgatatttcagTGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
||| | | | | | | | | | | || ||| || | | | | |||| | | || || |||||||| |||||| ||||| | || ||| | || | ||| |||||||| | || |||||||||||||||||||||||||| ||| |||||||||
--gtatgaatctctatttactgtttgtaatatacagcgtaacagacaagttattcatcctaaacgta-attgggtaa--cgttggttcttgatattacagTGGAGAAGGGGTCCCAGATCTCTTGCTGTGGTTGGTTCAATGGGCTCAGAAAACAATGGTTGAGAAACTTACATATGTTGACGAAGTGCAG
upper sequence: GLYMA10G37020.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G76820.1 (Arabidopsis thaliana), 3'ss of exon 5
ttttattagtgttgcctaaaactgttgcacaatctgcttaatgcttttcttgtgagtaatggtgttgtattgtctgagtttttattttttgatatttcagTGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
||| ||| | | | | | | | | || ||| || | | | | |||| | | || || |||||||| |||||| ||||| | || ||| | || | ||| |||||||| | || |||||||||||||||||||||||||| ||| |||||||||
--gtatgagtctctatttactgtttgtaatatacagcgtaacagacaagttattcatcctaaacgta-attgggtaa--cgttggttcttgatattacagTGGAGAAGGGGTCCCAGATCTCTTGCTGTGGTTGGTTCAATGGGCTCAGAAAACAATGGTTGAGAAACTTACATATGTTGACGAAGTGCAG
upper sequence: GLYMA10G37020.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G27700.2 (Arabidopsis thaliana), 3'ss of exon 3
ttttattagtgttgcctaaaactgttgcacaatctgcttaatgcttttcttgtgagtaatggtgttgtattgtctgagt--ttttattttttgatatttcagTGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACT---TACATACAGTGAAGAAGTGCAG
| | | || || ||| |||| ||||| | || ||||| |||| || ||||||||||||||| ||||| || || ||| | || || | ||| |||||| ||| || |||||||||||||||||||| |||||| ||| ||||||||
------------------------gtatatgagtctctctttg--tttattgtttgtaatttatcctaaatggttgagtaattttggttcttgatatttcagTGGGGAAGGGATCCCAGATCTATTGTTGTTGTTGGTTCAATTGACTCAGAAAACAATGGTTGAGAAACTAATTACATATGTTGACAAAGTGCAG
upper sequence: GLYMA10G37020.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0076g00310.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------ttttatta-gtgttgcctaaaactgttgcac-----aatctgcttaatgcttttcttgtgagtaatggtgttgtattgtctgagtttttattttttgatatttcagTGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
|| ||| | ||| | || || || | ||| | || | ||| || || | ||| | | | | | ||| | ||| | |||||||||||| || || || | || || ||||| |||| ||||| || |||||||||||||||||||| |||||||| |||||||||
gtatttctcatagcctctatgtctacccttgttatatcttgttccaggctcttcaactgaaaactctacaaaacgatttatttacaagcca--atgtcctgatattttgg-----attggtggatgta-cagTGGTGAAGGCATCCCAGACCTATTGCTATTATTGGTTCATTGGACTCAGAAAACAATGGTTGAGAAACTCACATACAGCAGTGAAGTGCAGMapped 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|208199933|gb|GD998620.1|GD998620EST: AACAAAGAAATGGGAGAAACGTTCAGCATTGTGCCTACAAGTGCAATAAG CGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAA
genomic: AACAAAGAAATGGGAGAAACATTCAGCATTGTGCCTACAAGTGCAATAAGgtaattgtaa ... gatatttcagTGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAA
EST:
gi|207706902|gb|GD689004.1|GD689004EST: AACAAAGAAATGGGAGAAACATTCAGCATTGTGCCTACAAGTGCAATAAG TGGTGAAGGAATTCCCGATTTGTTATTACTATTGAT
genomic: AACAAAGAAATGGGAGAAACATTCAGCATTGTGCCTACAAGTGCAATAAGgtaattgtaa ... gatatttcagTGGTGAAGGAATTCCCGATTTGTTATTACTATTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttgtgagtaatggtgttgtattgtctgagtttttattttttgatatttcagTGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
ttttgat putative branch site (score: 4)
ttttttg CT-rich tract
tgagtttttatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttattagtgttgcctaaaactgttgcacaatctgcttaatgcttttcttgtgagtaatggtgttgtattgtctgagtttttattttttgatatttcagTGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - -tgttgcc
- - - - - - - - - - - - -tgcacaa
- - - - - - - - - - - - - - - - tctgctt
- - - - - - - - - - - - - - - - - - - -aatgctt
- - - - - - - - - - - - - - - - - - - - - - - -tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtctg