Sequence
atgc intronic sequence ATGC exonic sequence...gccatttccaatgttaacaatgttcataatctttatcaaatcattacttgaattctttgtctgatatgtgatttttattttatattattattatactcagGTGGGCAGGGGTTACAGAAGCTAGAGGGGATTACCCATTTAGCCACCACAAATTAACTGTTCAGTTTTATGAAGCATCTGCTGCTCAGGATAGAAAGTTG
Basic information
species | Glycine max |
transcript | GLYMA19G24980.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G24980.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g55010.1 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------------gccatttccaatgttaacaatgtt-cataatctttatcaaa-tcattacttgaattctttgtctgatat-gtgatttttattttatattattattatactcagGTGGGCAGGGGTTACAGAAGCTAGAGGGGATTACCCATTTAGCCACCACAAATTAACTGTTCAGTTTTATGAAGCATCTGCTGCTCAGGATAGAAAGTTG
|| | | ||| | |||||| | || | ||| || |||| ||| | || || ||| | | | | | |||| || ||||||||| || || || |||| ||||||||| |||||||||||||||||| | ||||||||||||| || |||||||| || || ||||| || |||
gtgagtgtattctgaaactcgagtaactaattctttcacaaagggtcaccatttatttagatatatactgtcataaatgttgtacaacagagaaaaaaatctctactggaacatgcattaggaaattatgaaatgtctaactttccaatatt-tattcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGCCACCACAAACTTACTGTTCAGTTTTTAGAGGCATCTGCAGCACAAGATAGGAAATTG
upper sequence: GLYMA19G24980.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g07470.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------gccatttcca-atgttaacaatgttcataatctttatcaaatca------ttacttga--attctttgtctgat--atgtgatttttattttatattat--tattatactcagGTGGGCAGGGGTTACAGAAGCTAGAGGGGATTACCCATTTAGCCACCACAAATTAACTGTTCAGTTTTATGAAGCATCTGCTGCTCAGGATAGAAAGTTG
|| || | | || || | ||| | | | ||| | |||| || || | || | || || | || || | | | || | ||| | ||||||||| || || || || | ||||||||| |||||||||||||||||| | || || ||||||| || || ||||||||||| || || || |||
gtgagtgtattttggaacttgagtaacaaattctccgcggaggttgaagtgttcacatagataaagaacgaaaatattatacctgaaagaaagttgtctactagaacatgcattatgaaataaatataataattgtctacttttctgatatgtcattcagGTGGGTGGGCGTAGGTGATGCCACAGGGGATTATCCATTTAGCCACCACAAACTCACCGTCCAGTTTTCAGAGGCGTCTGCTGCTCAAGACAGGAAATTG
upper sequence: GLYMA19G24980.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G01780.1 (Arabidopsis thaliana), 3'ss of exon 3
gccatttccaatgttaacaatgttcataatctttatcaaatcattacttgaattctttgtctgatatgtgatttttattttatattat-tattatactc-agGTGGGCAGGGGTTACAGAAGCTAGAGGGGATTACCCATTTAGCCACCACAAATTAACTGTTCAGTTTTATGAAGCATCTGCTGCTCAGGATAGAAAGTTG
|| | | | | | ||| | |||| ||| || || || | || || | | | | | |||||| || |||||||| || |||| || | ||||| |||||||| ||||||||||| || | |||||||||||||| ||| |||| |||||||| || || || ||
------------gtgagctttcccttggcttgtaatccttttattatgtgagtt--ttactgcatttctggattggaactcagacaacctattattttccagGTGGGCTGGAGTTAGTGAGACAAGAGGAGATTACCCGTTTAGCCACCATAAGCTTACTGTTCAGTTTTACGAACCATCAGCTGCTCAAGACAGGAAATTA
upper sequence: GLYMA19G24980.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0171g00280.t01 (Vitis vinifera), 3'ss of exon 3
gccatttccaatgttaacaa-----tgttcataatctttatcaaatcattacttgaattctttgtctgatatgtgatttttattttatattattattatactcagGTGGGCAGGGGTTACAGAAGCTAGAGGGGATTACCCATTTAGCCACCACAAATTAACTGTTCAGTTTTATGAAGCATCTGCTGCTCAGGATAGAAAGTTG
||| || |||| | | | || || | | | | | | | | || || || | ||| | | | | || || | ||||||||| ||||||| ||| | ||||| ||||||||||||||||||||||| ||||| ||||||||||||||||||||||| |||||||| |||||||||
---attatgcattttaatacacttctatccaaaaatatcaagagaaaaaaattgcattttaatgactttt-tgtcacagtagtaatg-gttcttttcccttacagGTGGGCTGGGGTTAGTGAAACCAGAGGAGATTACCCATTTAGCCACCACAAGTTAACGGTTCAGTTTTATGAAGCATCTGCAGCTCAGGACAGAAAGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttgaattctttgtctgatatgtgatttttattttatattattattatactcagGTGGGCAGGGGTTACAGAAGCTAGAGGGGATTACCCATTTAGCCACCACAAATTAACTGTTCAGTTTTATGAAGCATCTGCTGCTCAGGATAGAAAGTTG
gtctgat putative branch site (score: 4)
tttgtctgatatgtga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccatttccaatgttaacaatgttcataatctttatcaaatcattacttgaattctttgtctgatatgtgatttttattttatattattattatactcagGTGGGCAGGGGTTACAGAAGCTAGAGGGGATTACCCATTTAGCCACCACAAATTAACTGTTCAGTTTTATGAAGCATCTGCTGCTCAGGATAGAAAGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
-ccatttc
- - - - caatgtt