Sequence
atgc intronic sequence ATGC exonic sequence...tttagctaagcctagatttattgtttgatggaagtgtttctttattaatctagttctcgtcataacaaacttaaattattgaattttgttgtatttatagTAGTAGCAGTGAAATGTCTACAAGGGACATACAAACCATCGTTCAAGCACTTCCACAGTACAGTGAACAAATTGATAAGCTCTCCCTCCATGTAGAG
Basic information
species | Glycine max |
transcript | GLYMA01G42140.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os04g18030.3 (Oryza sativa), 3'ss of exon 14
-ttta-gctaagcctagatttattgtttgatggaagtgtt-tctttattaatctagttctcgtcataaca-aacttaaattattgaattttgttgtatttat-agTAGTAGCAGTGAAATGTCTACAAGGGACATACAAACCATCGTTCAAGCACTTCCACAGTACAGTGAACAAATTGATAAGCTCTCCCTCCATGTAGAG
|| | | || | |||||| || | || || | || | | | || || | || || | || ||||| ||| |||| ||||| | || | | | | || | || || | || | |||| || |||||||| ||||| ||||||||||| |||||||| ||||| | || ||||| |||
gttaatggtattcaaagatttgttttatgttgaattaattatttctgttgataggatccttttctttttgtaatgtaaatgcttg-----tgttatatttgtcagAAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAG
upper sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 8
-tttagctaagcctagatttattgtttgatggaagtgtttctttattaatctagttctcgtcataacaaactta-aattattgaattttgttgtatttat-agTAGTAGCAGTGAAATGTCTACAAGGGACATACAAACCATCGTTCAAGCACTTCCACAGTACAGTGAACAAATTGATAAGCTCTCCCTCCATGTAGAG
|||| | | | || | ||| ||| ||| || |||| ||||| | | || | | | | |||| | |||| | ||| || | | | | || || || | || || | |||| || |||||||| |||||||||||||| || |||||||| ||||| || || ||||| |||
atttatttggacatgtatgttgagttgcatgagtccattttgtttgtaat---gttcttgacttattattttaatggtcattgcttcatgtttaaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG
upper sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 12
tttagctaagcctagatttattgtttgatggaagtgtttct---ttattaatctagttctcgtcataacaaacttaaattattgaattttgttgtatttatagTAGTAGCAGT---GAAATGTCTACAAGGGACATACAAACCATCGTTCAAGCACTTCCACAGTACAGTGAACAAATTGATAAGCTCTCCCTCCATGTAGAG
| | | | | | |||| | | |||| | || || | | | | | | || | | |||| |||| | | ||| | || | | | ||| | || ||||| || |||||| || ||||| || ||||||||||||||||| |||||||||||||| ||||| ||||| |||
---actgacttccaaacacgat-tttgttagctatgttcttaacttcttgtttcaatgttgat--ttgtaattaggattgattgcatttccctttcttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG
upper sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
tttagctaagcctagatttat-tgtttgatggaagt-gtttctttattaatctagttctcgtcataacaaacttaaatt-attgaattttgttgtatttatagTAGTAGCAGTGAAATGTCTACAAGGGACATACAAACCATCGTTCAAGCACTTCCACAGTACAGTGAACAAATTGATAAGCTCTCCCTCCATGTAGAG
||| | | ||| || || | | || | | | ||| ||| | ||| ||| || | || || || | | | || || ||| | | ||| | |||||||| || | || | || ||||||||| | ||||||||||||||||||||||| |||||||| ||||| ||||||
cttacattactctacgttgatctatgtggtatactttatttggttagagaagtaggtcttctctccttttgatcaattttgtttgactctttt---ttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG
upper sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 12
------tttagctaagcctagat----ttattgtttgatggaagtgtttctttattaatctagttctcgtcataacaaacttaaattattgaattttgttgtatttatagTAGTAGCAGTGAAATGTCTACAAGGGACATACAAACCATCGTTCAAGCACTTCCACAGTACAGTGAACAAATTGATAAGCTCTCCCTCCATGTAGAG
|| | | || | | || | |||||| ||||| | | | | | | | | | || || || |||| | | |||| | | || || | ||||| |||||||||||||| | |||| || |||||||| | ||||| || ||||| |||||||| ||||| ||||||||||| |||
atgtatctttgtgatatctggttaatctttctacttgatgccagtgtattcagaccagt--aatccaggatgtgttaacct--aaatattta--tctgttatgt----agAGGTGGTGGTGAATTGTCTACAAGGGACTTGCAAAAGATGGTTCAAGCTTTGCCACAATATAGTGAGCAAATTGAGAAGCTTTCCCTCCATGTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatctagttctcgtcataacaaacttaaattattgaattttgttgtatttatagTAGTAGCAGTGAAATGTCTACAAGGGACATACAAACCATCGTTCAAGCACTTCCACAGTACAGTGAACAAATTGATAAGCTCTCCCTCCATGTAGAG
tcataac putative branch site (score: 2)
ataacaaacttaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttagctaagcctagatttattgtttgatggaagtgtttctttattaatctagttctcgtcataacaaacttaaattattgaattttgttgtatttatagTAGTAGCAGTGAAATGTCTACAAGGGACATACAAACCATCGTTCAAGCACTTCCACAGTACAGTGAACAAATTGATAAGCTCTCCCTCCATGTAGAG
- - -ctaagcc
- - - - - - - - - - ttgtttg