Sequence
atgc intronic sequence ATGC exonic sequence...aattataggagaaaagaaaaatattccttaaaagttcctggtatttttctcttaaaaacaaaaagtaaattggagaataagacgtgtgctggtgacacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTGGCTACCCTGTATGTGATGACATTGACTCTCCCATCGGCAGCTGCA
Basic information
species | Glycine max |
transcript | GLYMA04G00640.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 3
-aattataggagaaaagaaaaatattccttaaaagttcctggtatttttctcttaaaaacaaaaagtaaattggagaataagacgtgtgctggtgacacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTGGCTACCCTGTATGTGATGACATTGACTCTCCCATCGGCAGCTGCA
| |||| | || | ||| || || | | || || | | || ||| | | |||| || || | ||||||||||||||||||||||||| || || || |||||||| || ||| | ||||| || |||| ||| |||| |||| || || ||||| | ||
tatctataaaacttgggagtag-attgattttaaccaaagtcaaaataacttatagtagtagtaattaagaaagtaattaagggatgaaatgcaaatgcagGGAGATAATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGCTGGCGACGGTGTACGTGCTGACGCTGACGCTGCCGTCGGCGTCGGCG
upper sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 5
------------------------------------aattataggagaaaagaaaaata--ttccttaaaagttcctggtatttttctcttaaaaacaaaaagtaaattggagaataagacgtgtgctggt-gacacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTGGCTACCCTGTATGTGATGACATTGACTCTCCCATCGGCAGCTGCA
| | || |||| ||| || | ||| | ||||| | | | || | || | | | || | || || ||| | ||||||||| |||||||||||||||||||| || || |||||| ||| ||| | |||| || ||||| ||| |||| |||| || || || || | ||
gtaagcctcagctgccagcagtctatatctatacccacacacagcagaagtgaagtttaggtcacttcagagttc--agagctacgtacgtacgtgatgagtgtcacagtgtgtgtacaa-atgggccggttggtgcagGGAGATCATGCACGCGATGTGGAAACCGCACAAGTTCAAGCTCATCTACCTGGTGGCGACGCTGTACGTGCTGACGCTGACGCTGCCGTCCGCCTCCGCC
upper sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G129413_T01 (Zea mays), 3'ss of exon 1
aattataggagaaaagaaa--aatattccttaaaagttcctggtatttttctcttaaaaaca-aaaagtaaattggagaataagacgtgtgctggtgacacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTGGCTACCCTGTATGTGATGACATTGACTCTCCCATCGGCAGCTGCA
| | | | | | || | | || || || | || || || | | || |||||||| ||||||||||||||| ||||| || ||||||||||| ||| | ||||| || ||||| ||| |||| |||| ||||| || || || ||
tgccaccgacacatgggtcccagcctgccacgaggcaccatgactcgttgcttccgttgttgtgtgcgcttctttttgacgttgatacatacatatg---tagGGAGATCATGCACGCGATGTGGCGTCCTCAGAAGTTCAAGGCCATCTACCTGCTGGCGACGCTGTACGTGCTGACGCTGACCCTCCCTTCCGCCGCCGCC
upper sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------aattataggagaaaagaaaaatattccttaaaagttc--ctggtatttttctct--taaaaacaaaaagtaaattggagaataagacgtgtgctggtgac--acagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTGGCTACCCTGTATGTGATGACATTGACTCTCCCATCGGCAGCTGCA
||| | | | || | ||| || |||| ||| | | |||| | | | | || || ||||| || | ||| ||||||||||| || |||||||||||||| || |||||| |||||||| | | || || || || ||| |||| | || || || || || ||||
gtatgttctcttttttttacccttttaaccccatcaccattcacatatcctaagggtataactggaattacagagtaatgaaaatgaccactcacttt---cattgtttgtgtgttgtttgttggcagAGAGATAATGCATGCTATGTGGAAACCTCAGAAGTTCAAGTCCATATACCTGTTTGCAACACTCTACGTGCTGACGCTAACGCTGCCTTCTGCGTCTGCG
upper sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 5
aattataggagaaaagaaaaatattccttaaaagttcctggtatttttctcttaaaaacaaa--aagtaaattggagaataagacgt-gtgctggtgacacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTGGCTACCCTGTATGTGATGACATTGACTCTCCCATCGGCAGCTGCA
| | | | || || || | ||| || |||| || || ||| |||| || | ||||| | | | | ||| ||||||||||| || ||||||||||| || |||||||||||||||||| | ||||||||| |||||||| ||||| |||| || || || || || |||
---ttttgaaaaacagtttccacttattccaaaattttaattattgtttagaaaattctaaatcaagtgtataaaaacataaggttttgatttttttttgcagAGAGATAATGCATGCAATGTGGAAACCACAGAAATTCAAGGCCATATACCTGCTGGCTACCGTGTATGTGCTGACACTGACACTTCCGTCCGCGGCAGCA
upper sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 5
aattataggagaaaagaaaaatattccttaaaagttcctggtatttttctcttaaaaacaaaaagtaaattggagaataagacgtgtgctggtgacacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTGGCTACCCTGTATGTGATGACATTGACTCTCCCATCGGCAGCTGCA
|| | || | | || | |||| | | | || || |||| || || | ||||||||| ||||||||||||||||| || ||||| |||||| | || | | |||||| | || || | || ||||| ||||| || || | |||
--------------------gtaagctttc---gcttctttcgctgttcttgcatggatcgatag-gcatcttctcataaactttgatctt----cccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
upper sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
aattataggagaaaagaaaaatattccttaaaagttcctggtatttttctcttaaaaacaaaaagtaaattggagaataag---acgtgtgctggtga-cacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTGGCTACCCTGTATGTGATGACATTGACTCTCCCATCGGCAGCTGCA
|| | || | | | || || | | | | | || ||| | | || | | ||||||||| ||||||||||||||||| || ||||| |||||| | || | | |||||| | || || | || ||||| ||||| || || | |||
--------------------gtaagctttcgcttctttcgctgttcttg-catggatcgataggctatgttgtcatcttttctcataaactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctcttaaaaacaaaaagtaaattggagaataagacgtgtgctggtgacacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTGGCTACCCTGTATGTGATGACATTGACTCTCCCATCGGCAGCTGCA
ttaaaaacaaaaagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattataggagaaaagaaaaatattccttaaaagttcctggtatttttctcttaaaaacaaaaagtaaattggagaataagacgtgtgctggtgacacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTGGCTACCCTGTATGTGATGACATTGACTCTCCCATCGGCAGCTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - -ggagaaaa
- - - - - - - - aaaaata
- - - - - - - - - - - - - - - - -gttcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtgct