Sequence
atgc intronic sequence ATGC exonic sequence...gcgtgcatgtttctatgcttagtatatcatttgcagttgccaaattaattgcctcttccttctatttctgactttgacctctagaaatatgttgttgtagATAGCTGGAGGGTTGTGTGACAATCTTCTGACATGTATTGTGAGAGCATGGGACTACAGCAAGCCACTGTTTGTTGCACCATCCATGAACTCTATTGTAT
Basic information
species | Glycine max |
transcript | GLYMA18G45650.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G45650.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g09910.2 (Oryza sativa), 3'ss of exon 2
---------------------------------gcgtgcatgtttctatgcttagtatatcatttgcagttgccaaattaattgcctcttccttctatttctgactttgacctctagaaatatgttgttgtagATAGCTGGAGGGTTGTGTGACAATCTTCTGACATGTATTGTGAGAGCATGGGACTACAGCAAGCCACTGTTTGTTGCACCATCCATGAACTCTATTGTAT
| | || ||| |||| | | | ||||| ||| ||| | | | ||| | | | |||| || || | ||||| |||| ||||| || || |||||||| || ||||||| || ||||||||||||||||||||||| ||||| |||||||| ||| | |||||| | | | |
gtatgtgattttcttttctttttctggtgtgaaccatatat-tttttatgttgaatcctggatttgt--ttgacaatgtcaacttgttttcgctgcctacaaaaaagtgaca-ctggattagttttgtt-cagATTGCTGGTGGTTTATGTGACAACCTCTTGACATGCATAGTGAGAGCATGGGACTACAGCAAACCACTCTTTGTTGCCCCAGCTATGAACACCTTCATGT
upper sequence: GLYMA18G45650.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G127911_T04 (Zea mays), 3'ss of exon 2
gcgtgcatgtttctatgcttagtatatcatttgcagttgccaaattaattgcctcttccttctatttctgactttgacctctagaaatatgttgttgtagATAGCTGGAGGGTTGTGTGACAATCTTCTGACATGTATTGTGAGAGCATGGGACTACAGCAAGCCACTGTTTGTTGCACCATCCATGAACTCTATTGTAT
| || | | ||| || | | || || | | | | ||||| || || || |||| | | ||| ||||| | | || | |||| || || ||||| || ||||| || |||| || || |||||||| |||||||||||||| || || |||||||| ||| |||||||| | | | |
----gtatatatatattttttttctctc-ttcgtggatagcgaattagtt------tcattgtattacacaaagtgatg-ctagat-tgttctgct-cagATCGCCGGTGGGTTATGCGACAACCTCTTGACCTGCATCGTGAGAGCGTGGGACTACAGCAAACCGCTCTTTGTTGCCCCAGCCATGAACACGTTAATGT
upper sequence: GLYMA18G45650.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G407396_T02 (Zea mays), 3'ss of exon 2
gcgtgcatgtttctatgcttagtatatcatttgcagttgccaaattaattgcctcttccttctatttctgactttgacctctagaaatatgttgttgtagATAGCTGGAGGGTTGTGTGACAATCTTCTGACATGTATTGTGAGAGCATGGGACTACAGCAAGCCACTGTTTGTTGCACCATCCATGAACTCTATTGTAT
|| | ||| || | | || || | | | | ||||| || || || |||| | | ||| ||||| | | || | |||| || || ||||| || ||||| || |||| || || |||||||| |||||||||||||| || || |||||||| ||| |||||||| | | | |
--------gtatatatattttttttctc-ttcgtggatagcgaattagtt------tcattgtattacacagagtgatg-ctagat-tgttctgct-cagATCGCCGGTGGGTTATGCGACAACCTCTTGACCTGCATCGTGAGAGCGTGGGACTACAGCAAACCGCTCTTTGTTGCCCCAGCCATGAACACGTTAATGT
upper sequence: GLYMA18G45650.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G18030.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------gcgtgcatgtttctatgcttagtatatcatttgcagttgccaaattaattgcctcttccttctatttctgactttgacctctagaaatatgttgt-----tgtagATAGCTGGAGGGTTGTGTGACAATCTTCTGACATGTATTGTGAGAGCATGGGACTACAGCAAGCCACTGTTTGTTGCACCATCCATGAACTCTATTGTAT
|| | ||| | | || | | | || ||| | | | | | | | | | | || | || | | |||||| ||||||| ||||| ||| | ||||| ||||||||||| || ||| | |||| |||||||| | ||| |||||||||||||| ||| | ||||| || | | |
gtaatttaacaaatcgacgaaaaccctaaaccaactac-ttagattcaattgtgtgacttgtgaaaacattcatggaggattcaattcatacaatatatttttgttgtacctttgtagATTGCTGGTGGGCTTTGTGATAATCTTCTGACTTGCATTATACGAGCTTGGGACTATACCAAACCACTGTTTGTTGCTCCAGCTATGAATACTTTGATGT
upper sequence: GLYMA18G45650.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G48605.1 (Arabidopsis thaliana), 3'ss of exon 2
gcgtgcatgtttctatgcttagtatatcatttgcagttgccaaattaattgcctcttccttctatttctgactttgacctctagaaatatgttgttgtagATAGCTGGAGGGTTGTGTGACAATCTTCTGACATGTATTGTGAGAGCATGGGACTACAGCAAGCCACTGTTTGTTGCACCATCCATGAACTCTATTGTAT
| || | || ||||| | | | ||| | || ||||| || ||| | | | | |||||||| |||| ||||| ||||| ||||| ||||| |||||||||| || ||||||||||| || ||||| || ||||||||||||| | |||||| || | | |
--------------gtact-aata-atcataggaaac-gtagctttagatctggattttagctatt--tggcttc-atatttgtttttttgttgttgcagATTGCTGGTGGGTTATGTGATAATCTATTGACATGTATAGTAAGAGCATGGGATTATAGCAAACCGTTGTTTGTTGCACCGGCGATGAACACTTTGATGT
upper sequence: GLYMA18G45650.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g10050.t01 (Vitis vinifera), 3'ss of exon 3
-gcgtgcatgtttctatgcttagtatatcatttgcagttgccaaattaattgcctcttccttctatttctgactttgacctctagaaatatgttgtt-gtagATAGCTGGAGGGTTGTGTGACAATCTTCTGACATGTATTGTGAGAGCATGGGACTACAGCAAGCCACTGTTTGTTGCACCATCCATGAACTCTATTGTAT
| || || ||| || | | ||| || || | ||| | ||| || | ||| | | | | | | || | | || |||||| || || || |||||||||| || |||||||| |||||| |||| |||||||||||||||||| |||||||||| ||| | |||||| | | | |
ttctgttgtgattttattttt--tttgccatgtggtgtgacacaatcataaatctcatcttgatatactcaattgtttctttactatatcttctatttgtagATTGCCGGGGGACTGTGTGACAACCTGCTGACATGCATTGTGCGAGCGTGGGACTACAGCAAGCCAATGTTTGTTGCGCCAGCTATGAACACCTTCATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taattgcctcttccttctatttctgactttgacctctagaaatatgttgttgtagATAGCTGGAGGGTTGTGTGACAATCTTCTGACATGTATTGTGAGAGCATGGGACTACAGCAAGCCACTGTTTGTTGCACCATCCATGAACTCTATTGTAT
tagaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcgtgcatgtttctatgcttagtatatcatttgcagttgccaaattaattgcctcttccttctatttctgactttgacctctagaaatatgttgttgtagATAGCTGGAGGGTTGTGTGACAATCTTCTGACATGTATTGTGAGAGCATGGGACTACAGCAAGCCACTGTTTGTTGCACCATCCATGAACTCTATTGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - gcatgtt
- - - - - - ctatgct
- - - - - - - - - - - - - - - - -cagttgc