Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgtggattacttgttgcttctgtctttgagatttaaatgtttatgacttcagcaacagaccctataccccttctctttctaacgcaagaagtgtttggttcagtgtccatccacttttgtttatcagatcatttattgaagtgcagattctgacttgcttcagtattgtctcagGTCCCAAGAAAGTTTACCAGTAAGGTTGAGGGAAAGATGGGATATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAACCTAGTC
Basic information
species | Glycine max |
transcript | GLYMA20G36530.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 8
gtttgtgtggattacttgttgcttctgtctttgagatttaaatgtttatgacttcagcaacagaccctataccccttctctttctaacgcaagaagtgtttggttcagtgtccatccacttttgtttatcagatcatttattgaagtgcagattctgacttgcttcagtattgtctcagGTCCCAAGAAAGTTTACCAGTAAGGTTGAGGGAAAGATGGGATATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAACCTAGTC
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---------------------------------------------------------------------------------------------gttagtatgttctattctgcatacagaactgagatgctg--ccttagttg--gcctaaatgttg--tttcctatatgtta-cttagGTCCCAAGAAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGATTTTGTTTACTTTATTTTGTCTGAGGAAGACAAATCATCCGAGCCTAGCC
upper sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 8
gtttgtgtggattacttgttgcttctgtctttgagatttaaatgtttatgacttcagcaacagaccctataccccttctctttctaacgcaagaagtgtttggttcagtgtccatccacttttgtttatcagatcatttattgaagtgcagattctgacttgcttcagtattg-tctcagGTCCCAAGAAAGTTTACCAGTAAGGTTGAGGGAAAGATGGGATATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAACCTAGTC
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----------------------------------------------------------------------------------gttagtctactcaattttagcatcaaaacc--ttagccctttattaccaaaatgttg--tgctttgtgtccttatattggcccttttactgcttttagATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGACTTTGTTTACTTTATATTATCAGAGGAAGACAAATCATCTGAGCCTAGTC
upper sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 8
gtttgtgtggattacttgttgcttctgtctttgagatttaaatgtttatgacttcagcaacagaccctataccccttctctttctaacgcaagaagtgtttggttcagtgtccatccacttttgtttatcagatcatttattgaagtgcagattctgacttgcttcagtattgtctcagGTCCCAAGAAAGTTTACCAGTAAGGTTGAGGGAAAGATGGGATATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAACCTAGTC
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-------------------------------------------------------------------------------gttagctactccacatctgcatttcttatttttaaaaaacttttttctactag-----ctgccgaatgtc--tttgtcactcggtctact----taatagGTACCGAGGAAGTTTACTAGTAAAACCGAAGGAAAGATGGGTTATGAGGATTTTGTTTACTTCATATTGGCTGAAGAAGACAAGTCATCAGAACCTAGTC
upper sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 8
gtttgtgtggattacttgttgcttctgtctttgagatttaaatgtttatgacttcagcaacagaccctataccccttctctttctaacgcaagaa--gtgtttggttcagtgt--ccatccacttttgtttatcagatcatttattg--aagtgcagattctgacttgcttcagtattgtctcagGTCCCAAGAAAGTTTACCAGTAAGGTTGAGGGAAAGATGGGATATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAACCTAGTC
||| || | | | || | || || |||| || | || | | || | | | | | | || | ||| || | || | || || | | | | | ||| || | | |||||| | | || | |||||| ||||||||||| ||||| || || ||||| |||||||| ||||| || || || | ||||| || ||||||||||| || || || ||||||||
----gtgcattctaatatccgacttgaatttcaaaatcta---gtttgggaaacttagcatggatgtaagaaatgtttcatgattgaagtgaagatcatgactatttctgtctagtaattcgctatttcaaagaaaaagaataattcctgagggttggttctga--taatgtggtgg-atttcagGTTCCAAGAAAGTTCACCAGCAAAGTAGAGGGGAAGATGGGTTATGAGGACTTCGTGTGGTTCATTCTTTCAGAAGAGGACAAGTCTTCAGAACCTAGCT
upper sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S34_411V6.1 (Physcomitrella patens), 3'ss of exon 8
gtttgtgtggattacttgttgcttctgtctttgagatttaaatgtttatgacttcagcaacagaccctataccccttctctttctaacgcaagaa-gtgtttggttcagtgtccatccacttttgtttatcagatcatttattgaagtgcagattctgacttgcttcagtattgtctcagGTCCCAAGAAAGTTTACCAGTAAGGTTGAGGGAAAGATGGGATATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAACCTAGTC
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------------------gtgcatttcgatgtaaaact---aggttcagcttttca-------aatttgcactcgatccgatttaacagtgagagtgtcttctctatagtgctaaagtaacactctaattccgttcaaggatttgaatgtaa-----tacgtggtgga------tgtcagGTTCCAAAAAGATTCACCAGCAAAGTTAAGGGAAAGATGGGTTATGAAGACTTTGTGTGGTTTATACTTTCAGAAGAGGACAAATCTTCAGAACCCAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatcagatcatttattgaagtgcagattctgacttgcttcagtattgtctcagGTCCCAAGAAAGTTTACCAGTAAGGTTGAGGGAAAGATGGGATATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAACCTAGTC
ttctgac putative branch site (score: 2)
ttgtctc putative PPT
atcatttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgtggattacttgttgcttctgtctttgagatttaaatgtttatgacttcagcaacagaccctataccccttctctttctaacgcaagaagtgtttggttcagtgtccatccacttttgtttatcagatcatttattgaagtgcagattctgacttgcttcagtattgtctcagGTCCCAAGAAAGTTTACCAGTAAGGTTGAGGGAAAGATGGGATATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAACCTAGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT