Sequence
atgc intronic sequence ATGC exonic sequence...gccatttccaatgttaacaatgttcataatcattatcaaatcatcaattgaattcattacgtgatatgtgattttaatcttatattatttttatactcagGTGGGCAGGGGTAACAGAAGCTAGAGGGGATTACCCATTTAGCCACCACAAATTAACTGTTCAGTTTTATGAAGCATCTGCTGCTCAGGATAGAAAGTTG
Basic information
species | Glycine max |
transcript | GLYMA16G06580.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G06580.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g55010.1 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------------gccatttccaatgttaacaatgtt-cataatcattatcaaatcatcaattga---attcattacgtgat-atgtgat-tttaatcttatattatttttatactcagGTGGGCAGGGGTAACAGAAGCTAGAGGGGATTACCCATTTAGCCACCACAAATTAACTGTTCAGTTTTATGAAGCATCTGCTGCTCAGGATAGAAAGTTG
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gtgagtgtattctgaaactcgagtaactaattctttcacaaagggtcaccatttatttagatatatactgtcataaatgttgtacaacagagaaaaaaatctctactggaacatgcattaggaaattatgaaatgtctaactttccaatattt----attcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGCCACCACAAACTTACTGTTCAGTTTTTAGAGGCATCTGCAGCACAAGATAGGAAATTG
upper sequence: GLYMA16G06580.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g07470.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------gccatttccaatgttaacaatgttcataatcattatcaaatcatcaattgaa---ttcattacgtgatatgtgattttaatcttatattatttttat-----actcagGTGGGCAGGGGTAACAGAAGCTAGAGGGGATTACCCATTTAGCCACCACAAATTAACTGTTCAGTTTTATGAAGCATCTGCTGCTCAGGATAGAAAGTTG
||| || | || | ||| | || | || | | | | ||||| | ||| | || |||| | || | || | || | ||||||||| || ||| || || | ||||||||| |||||||||||||||||| | || || ||||||| || || ||||||||||| || || || |||
gtgagtgtattttggaacttgagtaacaaattctccgcggaggttgaagtgttcacatagataaagaacgaaaatattatacctgaaagaaagttgtctactagaacatgcattatgaaataaat-ataataattgtctacttttctgatatgtcattcagGTGGGTGGGCGTAGGTGATGCCACAGGGGATTATCCATTTAGCCACCACAAACTCACCGTCCAGTTTTCAGAGGCGTCTGCTGCTCAAGACAGGAAATTG
upper sequence: GLYMA16G06580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G01780.1 (Arabidopsis thaliana), 3'ss of exon 3
gccatttccaatgttaacaatgttcataatcattatcaaatcatcaattgaattcattacgtgatatgtgattttaatcttatattattt-ttatactc-agGTGGGCAGGGGTAACAGAAGCTAGAGGGGATTACCCATTTAGCCACCACAAATTAACTGTTCAGTTTTATGAAGCATCTGCTGCTCAGGATAGAAAGTTG
|| | | | | | ||| | || | ||| || |||| || | || || | || | | | | |||| || |||||||| || || | || | ||||| |||||||| ||||||||||| || | |||||||||||||| ||| |||| |||||||| || || || ||
------------gtgagctttcccttggcttgtaatccttttattatgtgagtt--ttactgcatttctggattggaactcagacaacctattattttccagGTGGGCTGGAGTTAGTGAGACAAGAGGAGATTACCCGTTTAGCCACCATAAGCTTACTGTTCAGTTTTACGAACCATCAGCTGCTCAAGACAGGAAATTA
upper sequence: GLYMA16G06580.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0171g00280.t01 (Vitis vinifera), 3'ss of exon 3
gccatttccaatgttaacaa-----tgttcataatcattatcaaatcatcaattgaattcattacgtgatatgtgattttaatcttatattatttttatactcagGTGGGCAGGGGTAACAGAAGCTAGAGGGGATTACCCATTTAGCCACCACAAATTAACTGTTCAGTTTTATGAAGCATCTGCTGCTCAGGATAGAAAGTTG
||| || |||| | | | || || || | | | | ||||| ||| | ||| | || | | || |||| ||||||||| ||||| | ||| | ||||| ||||||||||||||||||||||| ||||| ||||||||||||||||||||||| |||||||| |||||||||
---attatgcattttaatacacttctatccaaaaatatcaagagaaaaa-aattgcattttaatgactttttgtcacagtagtaatg-gttcttttcccttacagGTGGGCTGGGGTTAGTGAAACCAGAGGAGATTACCCATTTAGCCACCACAAGTTAACGGTTCAGTTTTATGAAGCATCTGCAGCTCAGGACAGAAAGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattgaattcattacgtgatatgtgattttaatcttatattatttttatactcagGTGGGCAGGGGTAACAGAAGCTAGAGGGGATTACCCATTTAGCCACCACAAATTAACTGTTCAGTTTTATGAAGCATCTGCTGCTCAGGATAGAAAGTTG
ttttaat putative branch site (score: 3)
ttattttt putative PPT
tgatatgtgattttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccatttccaatgttaacaatgttcataatcattatcaaatcatcaattgaattcattacgtgatatgtgattttaatcttatattatttttatactcagGTGGGCAGGGGTAACAGAAGCTAGAGGGGATTACCCATTTAGCCACCACAAATTAACTGTTCAGTTTTATGAAGCATCTGCTGCTCAGGATAGAAAGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
-ccatttc
- - - - caatgtt
- - - - - - - - - - - - - - - - - - - - - - - - tgaattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatatg