Sequence
atgc intronic sequence ATGC exonic sequence...gcacattatgtatagcacaaattccataattttttcaatctaacaccagtgatctatatatggtgacaatcagttaacttggttatttctggtggaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
Basic information
species | Glycine max |
transcript | GLYMA06G23080.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 2
gcacattatgtatagcacaaattccataattt-tttcaatctaacaccagtgatctatatatggtgacaatcagttaacttggttatttctg---gtggaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
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--acattggcaacagttacatctgcgcatttgacttgtagtttgctctcgtcttttaattct--caaatgtttgtcttctgagatttacctgtccatgttacagTTTACCATGCCCTAAAGGGCATCATTAAGGCGAAATATGGTCAAGATGCATGCAATGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAG
upper sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G034848_T01 (Zea mays), 3'ss of exon 2
gcacattat----gtatagcacaaattccataattttttcaatctaacaccagtgatctatatatggtgacaatcagttaacttggttatttctggtggaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
|||| ||| | | | | |||||| | | | || | | || | | | ||| || | | || | | ||||||||| ||||| | ||||| || || |||||||||||||| ||||||||||| ||||| |||||||||||||| |||||||| ||||||||||| |||||
-tttgttataaaagtaaacatctatatttgggatttttgcttcttctagctggtcactt-catcttctatcc-tcacttggaata-tccttgttatggtaacagTTTACCATGTCCTGAAGGGCATCATTAAGGCAAAATATGGTCAAGATGCATGCAATGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAG
upper sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 2
gcacattatgtatagcacaaattccat---aattttttcaatctaacaccagtgatctatatatggtgacaatcagttaacttggttat-ttctggtggaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
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-tatgttgtatcagtgaatagctatattgggactatttgcttctgctagctggtcacttcatcttctaacc-tcacttggaatatccttgttctggt--aacagTTTACCATGTCCTGAAGAGCATCATTAAGTCAAAATATGGTCAAGATGCATGCAATGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAG
upper sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 2
-gcacattatgtatagcac--aaattccataattttttcaatctaacaccagtgatc-tatatatggtgacaat-cagttaacttggttatttctggtggaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
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catatttctcttttggttccaaagttcttctattctttggat-tatcacaaagaattgtttttctgatagtaatgcatttaatgtactt--tgttgatt--acagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG
upper sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 2
--gcac-attatgtatagcacaaattccataattttttcaatctaaca-ccagtgatctatatatggtgacaatcagttaacttggttatttctggtggaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
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ttctatgattatgcagttctttagtt--gtgatattgttgatgcaataatccatcataaatg-ataggaaagataaataaccatttttaatt-tgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccagtgatctatatatggtgacaatcagttaacttggttatttctggtggaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
agttaac putative branch site (score: 3)
atctatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcacattatgtatagcacaaattccataattttttcaatctaacaccagtgatctatatatggtgacaatcagttaacttggttatttctggtggaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - gcacaaa
- - - - - - - - - - - - - - - - - - - - -aacacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgac