Sequence
atgc intronic sequence ATGC exonic sequence...tgttttagtagagtaactagtttttacttaatttgacttttgtcatgtgctgaatttcacttaaatgaagttaatggatttcagattgtttgtatgctagGTATGAAGTTGACACAGATGCATTTCTTTCTGTTTTAGCCCTTCAACCAATTCCAAACATGGATTCTGTCCCCACCATTGTTGAG
Basic information
species | Glycine max |
transcript | GLYMA20G35310.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35310.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G43745.1 (Arabidopsis thaliana), 3'ss of exon 10
tgtttta------gtagagtaactagtttttacttaatttgacttttgtcatgtgctgaatttcacttaaatgaagttaatggatttcag-attgtttgtatgctagGTATGAAGTTGACACAGATGCATTTCTTTCTGTTTTAGCCCTTCAACCAATTCCAAACATGGATTCTGTCCCCACCATTGTTGAG
|||| | || |||| | | | | | | || || | | | || || | | | ||| | || | ||||||| |||||||||||||| ||||| |||||||||||||| || ||||||||||| || | ||| ||||| || |||| ||||| || |||
tgttctgaaacctgtcagaaaactggaatgctagtggtaaaagatatggaatct-caatactttgtaaaagaggaatcaattaagttaaacattgttt------cagGTATGAAGTTGATACAGACGCATTTCTTTCTGTATTGGCCCTTCAACCTATACAAAAGATGGAATCGATCCCAACCATAGTAGAG
upper sequence: GLYMA20G35310.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G02940.1 (Arabidopsis thaliana), 3'ss of exon 10
-------------------tgttttagtagagt--aactagtttttacttaatttgacttttgt-catgtgctgaa---tttcacttaaatgaagttaatggat---ttcagattgtttgtatgctagGTATGAAGTTGACACAGATGCATTTCTTTCTGTTTTAGCCCTTCAACCAATTCCAAACATGGATTCTGTCCCCACCATTGTTGAG
|| | || ||| | ||| | | | || | | | || | ||||| | ||| | || | | || || || | | | |||||||||||||| ||||| |||||||||||||| || |||||| |||| || | ||| ||||| || |||| |||||||| |||
gtaagaattaactacttctcattatggtttagtttgtttggttctgaatgaaaacaaagtataaatattttctgaaacctgtcagtagtttgtaaaagagaaatcaattaagttaaacattgtttcagGTATGAAGTTGATACAGACGCATTTCTTTCTGTATTGGCCCTTGAACCTATACAAAAGATGGAATCCATCCCAACCATTGTAGAG
upper sequence: GLYMA20G35310.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv05s0020g04630.t01 (Vitis vinifera), 3'ss of exon 10
--tgttttagtagagtaactagtttttacttaatttg-acttttgtcatgtgctgaatttcacttaaatgaagttaatggatttcagattgtttgtatgctagGTATGAAGTTGACACAGATGCATTTCTTTCTGTTTTAGCCCTTCAACCAATTCCAAACATGGATTCTGTCCCCACCATTGTTGAG
| ||| | || | | | || ||| || | | ||||||| || |||||| | ||||| ||||| | | | |||||||||||||| |||||||||||||| ||||| ||||||||||||| ||| |||| ||| ||||||||||||||||||||||
tcttgacaagtccatggtttaatctgtttacaagttgcacaaaccaaaattatcgaatttctct--gttgaagtctactgattttagatt-ctaatttatcagGTATGAAGTTGATACAGATGCATTTCTATCTGTACTAGCCCTTCAACCTATTTCAAAAATGACTTCTGTCCCCACCATTGTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgctgaatttcacttaaatgaagttaatggatttcagattgtttgtatgctagGTATGAAGTTGACACAGATGCATTTCTTTCTGTTTTAGCCCTTCAACCAATTCCAAACATGGATTCTGTCCCCACCATTGTTGAG
agttaat putative branch site (score: 4)
ttaaatgaagttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttttagtagagtaactagtttttacttaatttgacttttgtcatgtgctgaatttcacttaaatgaagttaatggatttcagattgtttgtatgctagGTATGAAGTTGACACAGATGCATTTCTTTCTGTTTTAGCCCTTCAACCAATTCCAAACATGGATTCTGTCCCCACCATTGTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - tgtcatg
- - - - - - - - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgaag