Sequence
atgc intronic sequence ATGC exonic sequence...aatattccttaaactttgctggtttttttgttgttaaaaaaataatgatattcttccaagttaattgctggagtgaataagacgtgtgttggtggcacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTTGCTACCCTGTATGTGATGACATTGACTCTTCCATCGGCAGCTGCA
Basic information
species | Glycine max |
transcript | GLYMA06G00690.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G00690.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 3
aatattccttaaactttg--ctggtttttttgttgttaaaaaaataatgatattcttccaagttaattgctggagtgaataagacgtgtgttggtggcacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTTGCTACCCTGTATGTGATGACATTGACTCTTCCATCGGCAGCTGCA
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--tatctataaaacttgggagtagattgattttaaccaaagtcaaaataacttatagtagtagtaattaagaaagtaattaagggatgaaatgcaaatgcagGGAGATAATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGCTGGCGACGGTGTACGTGCTGACGCTGACGCTGCCGTCGGCGTCGGCG
upper sequence: GLYMA06G00690.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 5
--------------------------aatattccttaaactttgc-----tggtttttttgttgttaaaaaaat---aatgatattcttccaagttaattgctggagtgaata-agacgtgtgttggt-ggcacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTTGCTACCCTGTATGTGATGACATTGACTCTTCCATCGGCAGCTGCA
| | | | || || || ||| || | | | | | | | | | | | | | || |||| | | | || | ||| || ||||||||| |||||||||||||||||||| || || |||||| ||| ||| | | || || ||||| ||| |||| |||| || || || || | ||
gtaagcctcagctgccagcagtctatatctatacccacacacagcagaagtgaagtttaggtcacttcagagttcagagctacgtacgtacgtgatgagtgtcacagtgtgtgtacaaatgggccggttggtgcagGGAGATCATGCACGCGATGTGGAAACCGCACAAGTTCAAGCTCATCTACCTGGTGGCGACGCTGTACGTGCTGACGCTGACGCTGCCGTCCGCCTCCGCC
upper sequence: GLYMA06G00690.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------aatattccttaaactttgctggtttttttgt-tgttaaaaaaataa-tgatattctt------ccaagttaattgctggagtgaataagacgtgtgttggtggc--acagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTTGCTACCCTGTATGTGATGACATTGACTCTTCCATCGGCAGCTGCA
|| | || ||| || | | ||| |||| || ||| || | | || | || |||||||| | | ||| ||||||||||| || |||||||||||||| || |||||| |||||||| | |||| || || || ||| |||| | || || || || || ||||
gtatgttctcttttttttacccttttaaccccatcaccattcacatatcctaagggtataactggaattacagagtaatgaaaatgaccactcactttcattgtttgtgtgttgtttgttggcagAGAGATAATGCATGCTATGTGGAAACCTCAGAAGTTCAAGTCCATATACCTGTTTGCAACACTCTACGTGCTGACGCTAACGCTGCCTTCTGCGTCTGCG
upper sequence: GLYMA06G00690.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 5
aatattccttaaactttgctggtttttttgttgttaaaaaaataatg-atattcttccaagttaattgctggagtgaataagacgt-gtgttggtggcacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTTGCTACCCTGTATGTGATGACATTGACTCTTCCATCGGCAGCTGCA
| || || || | || || || || || | | | ||| || | || || | ||||| | | || | ||| ||||||||||| || ||||||||||| || |||||||||||||||||| | || |||||| |||||||| ||||| |||| ||||| || || || |||
--ttttgaaaaacagtttccacttattccaaaattttaattattgtttagaaaattctaaatcaagtgtataaaaacataaggttttgatttttttttgcagAGAGATAATGCATGCAATGTGGAAACCACAGAAATTCAAGGCCATATACCTGCTGGCTACCGTGTATGTGCTGACACTGACACTTCCGTCCGCGGCAGCA
upper sequence: GLYMA06G00690.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 5
aatattccttaaacttt-gctggtttttttgttgttaaaaaaataatgatattcttccaagttaattgctggagtgaataagacgtgtgttggtggcacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTTGCTACCCTGTATGTGATGACATTGACTCTTCCATCGGCAGCTGCA
||| |||| ||| ||| |||| || | || |||| | | | || |||| || | | ||||||||| ||||||||||||||||| || ||||| |||||| | || | | |||||| | || || | || ||||| || || || || | |||
--------gtaagctttcgcttctttcgctgttcttgcatggat--cgata---------ggcatcttct------cataaactttgatctt----cccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
upper sequence: GLYMA06G00690.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
aatattccttaaacttt-gctggtttttttgttgttaaaaaaataatgatattcttccaagttaattgctggagtgaataagacgtgtgttggtggcacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTTGCTACCCTGTATGTGATGACATTGACTCTTCCATCGGCAGCTGCA
||| |||| ||| ||| |||| || | || |||| || || | | | | || | || | | | ||||||||| ||||||||||||||||| || ||||| |||||| | || | | |||||| | || || | || ||||| || || || || | |||
--------gtaagctttcgcttctttcgctgttcttgcatggat--cgataggctatgttgtcatcttttctcataaac------tttgatctt--cccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatattcttccaagttaattgctggagtgaataagacgtgtgttggtggcacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTTGCTACCCTGTATGTGATGACATTGACTCTTCCATCGGCAGCTGCA
agttaat putative branch site (score: 4)
aagttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatattccttaaactttgctggtttttttgttgttaaaaaaataatgatattcttccaagttaattgctggagtgaataagacgtgtgttggtggcacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTTGCTACCCTGTATGTGATGACATTGACTCTTCCATCGGCAGCTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - tgctggt
- - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acgtgtg