Sequence
atgc intronic sequence ATGC exonic sequence...gccatttctacgtactagtaatagttgccaccagttttttagtctatatgtgtatgctaagccagagttttgaattaactttatctttgtatatatttagACCAGATCGAGAAAGTGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCATCAAGTTAAAGCAGTTCTTGAGGAG
Basic information
species | Glycine max |
transcript | GLYMA19G02260.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 14
---------------gccatttctacgtactagtaatagttgccaccagttttttagtctatatgtgtatgctaagccag-------agttttgaattaactttatc---tttgtatatatttagACCAGATCGAGAAAGTGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCATCAAGTTAAAGCAGTTCTTGAGGAG
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gtaagccaatccagaattagctgtctgtgcaagtttattcttctattggcttgccacaattcgcaaacttgttaatttagtcagtttgatcttctatttactcaaccaaatttatat-tatctagGTCTGGCCGGGAAAGTGACAGTGATGCTGAGGATTTGGAGCATATTGAAAAGCTTCGTCAAGTCAAAGCAGTACTGGAGGAG
upper sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 15
gccatttctacgtactagtaatagttgcca-ccagttttttagtctatatgtgtatgctaagccagagttttgaattaactttatctttgtat-atatttagACCAGATCGAGAAAGTGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCATCAAGTTAAAGCAGTTCTTGAGGAG
||| || | || | | | ||| | || | || || | | | | || | | | ||| | ||| | || |||||| ||| | |||||||||||||| || ||||| |||| || ||||| ||||||| ||||||||||| |||||||| |||
--tattgacgaatatgcttcattgacattaactagtgatgtaattcatgagtacaattttaaatctggcaactaacttattgtatttatgtttgatgtttagATCAGGT---GAAAGTGATAGTGATGCAGAAGACCTTGAACACGCTGACAAGCTTCGGCAAGTTAAAGCCGTTCTTGAAGAG
upper sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 15
-------------------------------------------------------------------------gccatttctacgtactagtaatagttgccaccagttttttagtctatatgtgtatgctaagccagagttttgaattaactttat------ctttgtatatatttagACCAGATCGAGAAAGTGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCATCAAGTTAAAGCAGTTCTTGAGGAG
||||| | | | ||| | | | | | || | || | | | | | ||| |||| | || | ||| |||||||||| ||| |||||||||||||| || ||||| |||| |||||||| ||||||| |||||||||||||| ||||| |||
gtaccaaaaacatgtcttaatagtaacatgtcttagtccaaatctttcgaaggggattttgtctatcccgttgaagttttcttagaaacaaaggagcatgcttcatttactactgatagaaatcgtgtttacagttgaaatctagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG
upper sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 14
gccatttctacgtactagtaatagttgccaccagttttttagtctatatgtgtatgcta--agccagagttttgaattaactttatctttgtatat-atttagACCAGATCGAGAAAGTGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCATCAAGTTAAAGCAGTTCTTGAGGAG
| | | | | | | || | | | || |||| || | || | | || |||| ||| | || |||| ||||||||| | |||||||||||| ||||| || |||||| |||||||||||||||| |||| ||||||||||||||| ||||| |||
--taactgaaaatggcaaacacacttttaatttgcatattgactcttatgc-taggatagcattaatgattatgaactaatgacaaaatttcatattatttagACCTGGTCGAGAAAGTGACAGTGAAGCAGAAGATCTTGAGCATGCTGAAAAACTTCGTCAAGTTAAAGCAGTCCTTGAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgtgtatgctaagccagagttttgaattaactttatctttgtatatatttagACCAGATCGAGAAAGTGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCATCAAGTTAAAGCAGTTCTTGAGGAG
aattaac putative branch site (score: 2)
agttttgaattaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccatttctacgtactagtaatagttgccaccagttttttagtctatatgtgtatgctaagccagagttttgaattaactttatctttgtatatatttagACCAGATCGAGAAAGTGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCATCAAGTTAAAGCAGTTCTTGAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
-ccatttc
- - - - - - - - - - - - -tgccacc
- - - - - - - - - - - - - - - - - - - - - - - - - -gtatgct