Sequence
atgc intronic sequence ATGC exonic sequencegtatggattggagaccttgttgtcttttctaactgtattgtggaacatataatttccagatgaataaacttttactggatatgattgtttttattttaaccattcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCTTTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGGTTTGCTGCAGCTGC
Basic information
species | Glycine max |
transcript | GLYMA16G24310.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G24310.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 4
gtatggattggagaccttgttgtcttttctaactgtattgtggaacatataatttccagatgaataaacttttactggatatgattgtttttattttaaccattcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCTTTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGGTTTGCTGCAGCTGC
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gtatgaa---aaaacttcagaaattctgctggacgctgaacatctgaactagtttct-gtcgctcata---ttactctaaacggttgatattctcttc-caacttgacagGTTTAGCTGCTCCAGCAATTGCTGCAGGGTTTGGTGCTCTTGCTCCAACCCTGGGCACACTTGTCCCTGTTATAGGAGCTAGCGGATTTGCTGCTATGGC
upper sequence: GLYMA16G24310.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G092776_T04 (Zea mays), 3'ss of exon 6
gtatggattggagaccttgttgtcttttctaactgtattgtggaacatataatttccagatgaataaacttttactggatatgattgtttttattttaaccattcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCTTTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGGTTTGCTGCAGCTGC-----------------------------------------------------
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-----------------------------------------------------------------------gtgattcatatgctctaattctcttcgacc---cgacaggtttagctgcaccagccattgctgcaggatttggtgctctagctccaacactgggcacacttgtccctttcatagGGGCTAGTGGATTTGCTGCTATGGCTGCTGCGGCAGGATCTGTTGCTGGCTCTGTGGCAGTTGCTGCCTCATTTGGAG
upper sequence: GLYMA16G24310.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G092776_T07 (Zea mays), 3'ss of exon 5
gtatggattggagaccttgttgtcttttctaactgtattgtggaacatataatttccagatgaataaacttttactg--gatatgattgtttttattttaacc-attcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCTTTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGGTTTGCTGCAGCTGC
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gta-ggactgcgttccagatcatgtat-ctaa-tgaaatgctgaacatcttggcatcatttggacacactacaccaggtgattcatatgctctaattctcttcgacccgacagGTTTAGCTGCACCAGCCATTGCTGCAGGATTTGGTGCTCTAGCTCCAACACTGGGCACACTTGTCCCTTTCATAGGGGCTAGTGGATTTGCTGCTATGGC
upper sequence: GLYMA16G24310.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 4
gtatggattggagaccttgttgtcttttctaactgtattgtggaacat-ataatttccagatgaataaacttttactggatatgattgtttttattttaaccattcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCTTTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGGTTTGCTGCAGCTGC
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---------gcaaccatagtaggacgtagtaaatatgaaatttctcttcaaaagcttcagacagcatgactgtttttgacttt--tcagttcatttttcactcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccagatgaataaacttttactggatatgattgtttttattttaaccattcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCTTTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGGTTTGCTGCAGCTGC
ttttaac putative branch site (score: 2)
atatgattgtttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggattggagaccttgttgtcttttctaactgtattgtggaacatataatttccagatgaataaacttttactggatatgattgtttttattttaaccattcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCTTTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGGTTTGCTGCAGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC