Sequence
atgc intronic sequence ATGC exonic sequence...ttgttctgtcgtttgtgtctcaaggtgtgggctatctatcatttgtgcattaaatagtttcttcttttacatctgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
Basic information
species | Glycine max |
transcript | GLYMA01G42960.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 3
ttgttctgtcgtttgtgtctcaaggtgtgggctatct-atcatttgtgcattaaatagtttcttcttttacatctgatttagtttaact-tctg--atccata---gTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
| || |||| || | | |||| | || | || || | | | | || | || |||| || | ||| | |||| || || |||| | ||||| |||||||||||||||||||| || ||||| ||||| ||| ||||||||| |||||||| | || | | ||
------tatcctttgagtagtgtgccactgactattttattaggactg-atcatcctttgtttctcttcaaatttgatataatataattctctgtcatttgtatcagTGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAG
upper sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
ttgttctgtcgttt---gtgtctcaaggtgtgggctatctatcatttgtgcattaaatagtt-tcttcttttacatctgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
| ||| || | | ||||| ||| ||| | | |||| | ||| || || || | | | || | ||| | || |||| | ||||| |||||||| ||||||||||| |||||||| ||||||||| ||||||||| |||||||| |||| || ||||
-taatctaacggatcaggagtctcgct-tgtacgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaattgtttattgtcatctatttca--gTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
upper sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 2
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
------ttgttctgtcgtttgtgtct-caaggtgtgggctatctatcatttgtgcattaaatagtttcttcttttacatctgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
| || || | ||| | | || | | | | | || ||| ||||| | ||||| | ||| || || | ||| | ||| | || |||| || ||||| |||||||| ||||||||||| || ||||| ||||||||| ||||||||| |||||||| |||| || ||||
ataactctaaactatcatctgtcttgactagctaaatgttttattgcacttggtcattattt-gtttccttatttgaatt--gttca--ttatcatctatttca--gTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
upper sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 2
ttgttctg--tcgtttgtgtctcaaggtgtgggctatctatcatttgtgcattaaatagtttcttcttttacatctgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
| ||| | ||| || ||| | | | || | | | ||| || | || | | | ||| | || | ||| ||||||||||| ||||||||||| ||||| ||||| ||||| | ||||||||| |||| |||||||| ||||| |||||| | || |||
ataaactgatttgttctcttcacaaaatattgaatagg-agaactcaaatgttatatttctatgtcacccctgttttgatcggtt-atgttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA
upper sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g03850.t01 (Vitis vinifera), 3'ss of exon 1
ttgttctgtcgtttgtgtctcaaggtgtgggctatctatcatttgtgcattaaatagtttcttcttttacatctgatttagtttaactt--ctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
| || | ||||| | | | | | || |||| |||| | ||| | || | | | || || ||| ||| || || | |||||||||||| ||||||||||||||||||||||| || | |||||||||||||| || |||| ||||||||| || || || ||||||
gattgcttgcatttgtctatttaatt-taagcaatctgctatttct-catgcattattctttataattctgactttttttttttcttttgcttggactttagTGAAAGTGGGGAGATGTGTGCAATGAAGGAGGTTACATTATTTTCAGATGATGCGAAGTCAAAGGAAAGTGCACAGCAGCTGGGCCAA
upper sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 4
---ttgtt-ctgtcgtttgtgtctcaaggtgtgggctatctatcatttgtgcattaaatagtttcttcttttacatctgatttagtttaactt--ctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
| || || | ||||| | | || | | || |||| |||| | ||| | || | || || |||||| || ||| || || | |||||||||||| ||||||||||||||||||||||| || | |||||||||||||| || |||| ||||||||| || || || ||||||
cagtgattgcttgcatttgtctatttagtt-taagcaatctgctatttct-catgca----ttattctttatatatctgactttttttcttttgcttggactttagTGAAAGTGGGGAGATGTGTGCAATGAAGGAGGTTACATTATTTTCAGATGATGCGAAGTCAAAGGAAAGTGCACAGCAGCTGGGCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcattaaatagtttcttcttttacatctgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
ttctgat putative branch site (score: 3)
cttct CT-rich tract
atttagtttaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttctgtcgtttgtgtctcaaggtgtgggctatctatcatttgtgcattaaatagtttcttcttttacatctgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- -ttctgtc
- - - - - gtttgtg
- - - - - - - - - - - - gtgtggg
- - - - - - - - - - - - - - - - - - - - - - -tgcatta