Sequence
atgc intronic sequence ATGC exonic sequence...gataccaactatgtttggcatatttaaacttggttgccccttcatgatatcatctctccagttttcctttaatgcaatctttccatttaggtgatttcagACTGAACTTGCTAGGGAGATGGGATATGCTGCTGCAAGATTTGGGCATGTAATGTTCCCTGAGAATGTTCATGAGCCAGCCTTGAATTGTGCTGAGCTTT
Basic information
species | Glycine max |
transcript | GLYMA13G01170.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G01170.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g14770.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------gataccaactatgtttggcatatttaaacttggttgccccttcatgatatcatctctccagttttcctttaatgcaatctttccatttaggtgatttcagACTGAACTTGCTAGGGAGATGGGATATGCTGCTGCAAGATTTGGGCATGTAATGTTCCCTGAGAATGTTCATGAGCCAGCCTTGAATTGTGCTGAGCTTT
| |||||| || | | || | || | || ||| | | | ||| ||| || || | || | | ||| ||| ||||||||| || || ||||| |||||||||||||| | ||| ||||| ||||| || |||||||||||||| || || | |||||| || ||||
gttattgtctacacatcttccatcatccgtgaaatttcttgtcttctcgtttgctaagggaactattgttagtagtgttttatttctaaagctctgtatgttgaacttttgacaggcaatttttgtagcctaaatttctctttgctcatt--agATTGAACTTGCAAGAGATATGGGTTATGCTGCTGCAAGGTATGGTCATGTGATGTTTCCAGAGAATGTTCATGAACCTGCTCTTCGTTGTGCAGAACTTT
upper sequence: GLYMA13G01170.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G102156_T02 (Zea mays), 3'ss of exon 4
------------------------------------------------------------------------------------------gataccaactatg-tttggcatatttaaacttggttgcccc--ttcatgatatcatctctccagttttcctttaa--tgcaatctttccatttaggtgatt--tcagACTGAACTTGCTAGGGAGATGGGATATGCTGCTGCAAGATTTGGGCATGTAATGTTCCCTGAGAATGTTCATGAGCCAGCCTTGAATTGTGCTGAGCTTT
| | | | | || | | || || || ||| | || | | ||| | || | || | | || | | | | ||| ||||||||| || || ||||| |||||||| ||||||| ||| ||||| ||||| || ||||||||||||||||| || | ||| ||| || |||
gttttgtcctcacagatctggatatgtgttttatttcacatcttcttatttttgctacaagaactcccttttacactttttattggtaaagttgtgtattttaacttttgacaagcaatttttgtagcctaaacttgtggaacttttgacaggacttttttgtagcctaaaaccctaaacttctctttactcattagATTGAACTTGCAAGAGATATGGGCTATGCTGCCGCAAGATATGGTCATGTGATGTTTCCAGAGAATGTTCATGAGCCTGCTCTTCATTCTGCGGAAGTTT
upper sequence: GLYMA13G01170.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G57590.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------gataccaactatgtttggcatatt------taaactt----ggttgccccttcatgatatcatctctccagttttcctttaatgcaatctttccatttaggtgatttcagACTGAACTTGCTAGGGAGATGGGATATGCTGCTGCAAGATTTGGGCATGTAATGTTCCCTGAGAATGTTCATGAGCCAGCCTTGAATTGTGCTGAGCTTT
||| || | || |||| || | || | || || || || || | || || ||| || ||| || |||||| |||||| |||| |||||||| || ||||| || ||||||| || ||||||||||| ||||||||||||||||| |||| || |||||||| || |||||||| |
gtcatctgtgcccattatttcccagttttatgacaaatatcagttccacgtgcattattatgtcatagattttaatgcttacctctctttgtgatgaatcttctgaagtttattt--tgaaatttt---gtttaggctgtttcagGCTGAGCTTGCTAGAGAAATGGGTTACACTGCTGCTAGGTTTGGGCATGTTATGTTCCCTGAGAATGTATATGAACCTGCCTTGAAGTGCGCTGAGCTGT
upper sequence: GLYMA13G01170.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0052g01390.t01 (Vitis vinifera), 3'ss of exon 4
gataccaactatgtttggcatatttaaac--ttggttgccccttcat-gatatcatctctccagttttcctttaatgcaatctttccatttaggtgatttcagACTGAACTTGCTAGGGAGATGGGATATGCTGCTGCAAGATTTGGGCATGTAATGTTCCCTGAGAATGTTCATGAGCCAGCCTTGAATTGTGCTGAGCTTT
| | | | || || ||| || | | | | | | | | ||| |||| | | |||||||| ||||||| ||| ||||| || || |||| |||||||||||||||||||||||||||||||| |||||||||||| |||||||||| || | ||||| || ||||
---gttgagtctttgcataatgccagaatcattgattttatttgcttcaaaagtgtgttggtaagtttgtcttaactgtggttatttgtttaggtggtttcagATTGAGCTTGCAAGAGATGTGGGTTATGCTGCTGCAAGATTTGGGCATGTAATGTTTCCTGAGAATGTTTATGAGCCAGCTTTAGAATGTGCAGAACTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatatcatctctccagttttcctttaatgcaatctttccatttaggtgatttcagACTGAACTTGCTAGGGAGATGGGATATGCTGCTGCAAGATTTGGGCATGTAATGTTCCCTGAGAATGTTCATGAGCCAGCCTTGAATTGTGCTGAGCTTT
ctttaat putative branch site (score: 4)
tttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gataccaactatgtttggcatatttaaacttggttgccccttcatgatatcatctctccagttttcctttaatgcaatctttccatttaggtgatttcagACTGAACTTGCTAGGGAGATGGGATATGCTGCTGCAAGATTTGGGCATGTAATGTTCCCTGAGAATGTTCATGAGCCAGCCTTGAATTGTGCTGAGCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - ccaacta
- - - - - - - - - - - - - - - - - - ccccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccattta