Sequence
atgc intronic sequence ATGC exonic sequence...gttaatctctccctcccccttctcccaatttacatacaggggattttttctcacaatgagatgttgtagttatactctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
Basic information
species | Glycine max |
transcript | GLYMA12G30520.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 8
------------------------------------------------------------gttaatctctccctcccccttctccca-atttacata--------caggg-----gattttttctcac---aatgagatgttg-tagttatactct-------ctattctgattgctat--att-cagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
| | ||| | |||| || | ||| | | | || || | ||| ||| | | | || | | | | | | || ||| | | || ||| |||| |||||||||||||||||||| ||||||||||| ||||| |||||||||||||| || |||||||| || || |||||||| ||| | ||||||||
gtgagttcaaacgaaaacttctactactatatattttaatttctagcaatttgtttctcaaccagttcctcaccttccctacttttatattcatacaattatcttcatggtctccagtgtttcaccactggagtaaaataaagcttatcacgcatttagaatgcttctctaagttctcccgattatagGTTATGCATCTTGATGCTGAAAAGGAGATGATGTCCCAGTGCGTGGCTCTTCTTGGGAAGTTTATTGCAGTTCGGGAACCAAATATTAGGTATCTTGGTC
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 9
gttaatctctccctcccccttctcccaatttacatacaggggattttttctcacaatgagatgttgtagttatactctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
|| | | | | | | ||| | |||| | | ||| | | | | | || ||| | |||| | ||| || |||| |||||||| ||||||||||| ||||||||||| |||||||||||||||||||| || |||||||| ||||| || ||||||||||| || |||||
gtgagtttgtacttatgt-ttcgcaaaattacagtttggtatattgtctttttaattaagtctttgcacgtataat-------------gcttcatatagGTCATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTC
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 8
-------------------------------------------gttaatctctccctcccccttctccc--aatttaca-tacaggggattttttctcacaatgagatgttgtagttatac---tctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
|||| | | || |||| | | |||| | | || | || | | || ||| | | || | | || || |||| |||||||| |||||||| || ||||||||||| |||||||||||||||||||| || |||||||| ||||| || ||||||||||| || || ||
gtgagtttgtattgactttaaagcgattaatcccccaccctggtccgatcttgcattgccttttctgcataagtttatgcttcgcaaaatcacagtttggtatcctgtctattaattaagtctgtttgcatgtataatactccatatagGTCATGCATCTGGATGCTGAGAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTCGGTC
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
gttaatctctccctcccccttctcccaatttacatacaggggattttttctcacaatgagatgttgtagt-tatactctctattctgattgctatattc------agGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
| | || || || | || ||| || || ||| | || |||| | | ||| || || | | || |||| ||||||||||||||||| || || |||||||| |||||||| ||||||||||| || |||||| |||||||||| || ||||| ||||||| ||||
-----tatttctaagaggtttatcatggatagttgactta--attgttcctaacagttctctggcttagtgtgcaacctcctaactttttaatgtgttttgatatagGTCATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCT
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 8
-gttaatctctccctcccccttctc---ccaatttacatac---aggggattttttctcacaatgagatgttgtagttatactctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
| || | | || | | | || || || || | ||| | | | || || || ||| || | || || |||| |||| ||||||||||||||||| || || |||||||| |||||||| ||||||||||| || |||||| |||||||||| || ||||| ||||||| ||||
aagagagcttttcttcgcgatgattagattgatgagcacactctagtaaactttctggcttagtg---tgcaaccccta-acttgttaatgtg-ttttgatat--agGTCATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCT
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 8
gttaatctctccctcccccttctcccaatttacatacaggggattttttctcacaa----tgagatgttgtagttatactctctattctgattgctatatt-cagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
| | || ||| | |||| | | | | | | || | | | | || | | | | | | | | ||| | | ||||| |||||||| |||||||||||||| ||||||||||| ||||| || | ||||| |||||||||||||| || || ||||| || ||||||||||| |
-----gttgggttttcctcttatttcaatgtgggtttaagatactggtttttatgagaattaaggagcttttatgtggttgtgtccttcaattaccctggcacagGTCATGCATCTGGATGCTGAAAAAGAAATGATGTCTCAATGTGTTGCCTTGCTTGGGAAATTTATTGCTGTACGAGAGCCAAATATACGATATCTTGGTT
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ34224 (Selaginella moellendorffii), 3'ss of exon 8
gttaatctctccctcccccttctcccaatttacatacaggggattttttctcacaatgagatgttgtagttatactctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
| | |||||||| | | |||| | | | | | || | | || |||||||||||| | || || || ||||| |||||| | || ||||| | ||| |||||||| ||||||||||||||||| || |||||||||||||||||
--------------------------------------gtaggttttttctttt--tctgttgttccattcaagagccttttttttgtcgcg-----cagGTGATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctcacaatgagatgttgtagttatactctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
tagttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaatctctccctcccccttctcccaatttacatacaggggattttttctcacaatgagatgttgtagttatactctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
- - -tctctcc
- - - - - - ctccccc
- - - - - - - - - -ttctccc
- - - - - - - - - - - - - - - -acataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattg