Sequence
atgc intronic sequence ATGC exonic sequence...agggtatcttgacaagaatatggttttagtaaagttcaaattttggaaatgcctttctgatttagagaaaaataaatttaatttcccttttttcttttagGCACTCAAGAGGAAGCAGCAGAAGCATACGATATAGCCGCAATAAAATTCCGCGGCGCGAATGCAGTCACAAACTTTGACATTTCAAGATACGATGTCGA
Basic information
species | Glycine max |
transcript | GLYMA06G05170.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G05170.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 8
agggtatcttgacaagaatatggttttagtaaagttcaaattttggaaatgcctttctgatttagagaaaaataaat--ttaatttcccttttttct-tttagGCACTCAAGAGGAAGCAGCAGAAGCATACGATATAGCCGCAATAAAATTCCGCGGCGCGAATGCAGTCACAAACTTTGACATTTCAAGATACGATGTCGA
| | | | | || | ||| | || ||| | ||||| | ||| | | ||||| | ||| | | | |||||||||||| ||||||||||| |||||||| || || || || || ||||| ||| ||| || || || ||||||||||| |||| ||||| || ||
actttgcagtaggatctacattggtttttggatgtataaac---aagatggccttattacaacggagcgtttccattggttaatctatttttatgcaatacagGCACTCAAGAAGAAGCAGCAGAGGCATACGACATTGCTGCCATCAAGTTCCGTGGCCTGAACGCGGTGACGAACTTTGACATCACAAGGTACGACGTGGA
upper sequence: GLYMA06G05170.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------------------agggtatcttgacaagaatatggtttta--gtaaagttcaaa---ttttggaaa-tgcctttctgatttagagaaaaataaatttaatttcccttttttcttttagGCACTCAAGAGGAAGCAGCAGAAGCATACGATATAGCCGCAATAAAATTCCGCGGCGCGAATGCAGTCACAAACTTTGACATTTCAAGATACGATGTCGA
|| | | || ||| | | || ||| ||| ||| | | |||| | | | || | |||| | || | | || | | | |||||| ||||||||||||||||| || ||||| || ||||| ||||||||||| || ||||| ||||||||||| ||||| || | ||| ||| |
gtgagtgccggtttcacatgaatttgtaaacattagtggattaccctcgctgcaaatcctggtcgtttctcctgataggacttctgatatcgattccggagacatcagcatattctgggtctcgttgcaatgttgaaaggatttcgcagggtgcccatgttacctaatgg---ttaaaatgaactggctttgtatgactcagGCACACAAGAGGAAGCAGCAGAGGCCTACGACATTGCCGCGATAAAATTCCGTGGAATCAATGCCGTCACAAACTTCGACATGTCTCGTTACAATGCTGC
upper sequence: GLYMA06G05170.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------------------------------------------agggtatcttgacaagaat---atggttttagtaaagttcaaattttggaaatgcctttctgatttagagaaaaataaatttaatttcccttttttcttttagGCACTCAAGAGGAAGCAGCAGAAGCATACGATATAGCCGCAATAAAATTCCGCGGCGCGAATGCAGTCACAAACTTTGACATTTCAAGATACGATGTCGA
|| | ||| | | | | | | |||| | | || |||| | | || || || | | | || | | | | | || ||||||||||||||||||||| || || ||||| ||||| || ||||||| || || ||||| |||||||||||| | || || | ||| | |
gtaagtgcaggtctcacatgaattcgtgcacagtagcggattactctcgctccatatagcggtcatttctcctgataggacttccgacgttgcttccagagacgtcggagtgttctggatctagatgtgcccatgttatcta---aatgtttgaataaactggc--tgtgtaattcagGCACTCAAGAGGAAGCAGCGGAGGCCTACGACATAGCTGCCATAAAATATCGTGGAATTAATGCCGTCACAAACTTTCATATCTCTCGTTACCTAGCTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaatgcctttctgatttagagaaaaataaatttaatttcccttttttcttttagGCACTCAAGAGGAAGCAGCAGAAGCATACGATATAGCCGCAATAAAATTCCGCGGCGCGAATGCAGTCACAAACTTTGACATTTCAAGATACGATGTCGA
tttaatttcccttttt CT-rich tract
atttagagaaaaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agggtatcttgacaagaatatggttttagtaaagttcaaattttggaaatgcctttctgatttagagaaaaataaatttaatttcccttttttcttttagGCACTCAAGAGGAAGCAGCAGAAGCATACGATATAGCCGCAATAAAATTCCGCGGCGCGAATGCAGTCACAAACTTTGACATTTCAAGATACGATGTCGA
- - - - -tgacaag
- - - - - - - - - - - - - - - - - - - - - - - -aatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa