Sequence
atgc intronic sequence ATGC exonic sequence...ggaggctcagattctttctgtagtctaatgaatataatttttctcaattaattaataaacaagttcttcctgtggaaatgacaatcatattcttgtccagATAACAGATGCAGTTGTTGTTGCAAGAATTCTTAATGCTACACTAGTTGTACCTGAGTTGGATCATCAATCTTTTTGGAAAGATGACAG
Basic information
species | Glycine max |
transcript | GLYMA05G04720.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G04720.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g46570.1 (Oryza sativa), 3'ss of exon 3
ggaggctcagattctttctgtagtctaatgaatataatttttctcaattaattaataaacaa-gttcttcctgtggaaatgacaatcatattcttgtccagATAACAGATGCAGTTGTTGTTGCAAGAATTCTTAATGCTACACTAGTTGTACCTGAGTTGGATCATCAATCTTTTTGGAAAGATGACAG
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-------------------gta--caactgtatttcaacttttt-attgcgttgctttgtattatccattgtattaccattacgatcttcagttt--ccagATAACAGATGCTGTTGTTGTCGCCCGAATATTGAATGCCACACTTGTTGTACCTGAGTTAGATCACCACTCATTCTGGAAGGATGATAG
upper sequence: GLYMA05G04720.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G101181_T03 (Zea mays), 3'ss of exon 3
ggaggctcagattctttctgtagtctaatgaatataatttttctcaattaattaataaacaagttcttcctgtggaaatgacaatcatattcttgtccagATAACAGATGCAGTTGTTGTTGCAAGAATTCTTAATGCTACACTAGTTGTACCTGAGTTGGATCATCAATCTTTTTGGAAAGATGACAG
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----gtatgattgccttccaatgtctggttgatttg-tttttatcatccctt----------gtgttaccttt----atgatgttcag---cttg--cagATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTTGTACCTGAGTTAGACCACCACTCGTTCTGGAAAGACGACAG
upper sequence: GLYMA05G04720.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------ggaggctcagattctttctgtagtc---taatgaatataatttttctcaat-taattaataaacaagttcttcc--tgtggaaatgacaatcatattcttgtccagATAACAGATGCAGTTGTTGTTGCAAGAATTCTTAATGCTACACTAGTTGTACCTGAGTTGGATCATCAATCTTTTTGGAAAGATGACAG
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gtaagtgaaattatgtgtcaagaataaacgtgttaggatattacaattatattgcttatttgcccaactaaaaaagattatgctgcttattgtccttagggagttaggacctgcattttgaaaataatgttc-tctttgtgtgcagATAACTGATGCAGTGGTTGTTGCACGGATTCTTAATGCTACTTTAGTTGTACCCGAGTTGGATCACCATTCTTACTGGAAAGATGACAG
upper sequence: GLYMA05G04720.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0229g00100.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------ggaggctcagattctttctgt---agtctaatgaatata------atttttctcaattaattaataaacaagttcttcc-tgtggaaatgacaatcatattcttgt--ccagATAACAGATGCAGTTGTTGTTGCAAGAATTCTTAATGCTACACTAGTTGTACCTGAGTTGGATCATCAATCTTTTTGGAAAGATGACAG
||| | | | || | || | | || || ||| | || | ||| ||| ||| | | || ||||| | |||||| ||| || |||||||| ||||| || || ||||| | ||||||||||||||| |||||||||| |||||||||||||| || || ||||||||||| ||
gtaagtataaagattcttctgtagctgctacatgttcattaaaacatatatagtggaaggatatgctgttgccgtgtcaacttcataaacatattataaacttgtttcagttatttacttgtttatcctttttgcatggaatttacaatccatttcctgcactcagATAACCGATGCTGTAGTAGTTGCTCGGATTCTTAATGCTACATTAGTTGTACCAGAGTTGGATCATCATTCCTTCTGGAAAGATGATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattaattaataaacaagttcttcctgtggaaatgacaatcatattcttgtccagATAACAGATGCAGTTGTTGTTGCAAGAATTCTTAATGCTACACTAGTTGTACCTGAGTTGGATCATCAATCTTTTTGGAAAGATGACAG
aattaat putative branch site (score: 3)
ttcttgtcc putative PPT
attaataaacaagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaggctcagattctttctgtagtctaatgaatataatttttctcaattaattaataaacaagttcttcctgtggaaatgacaatcatattcttgtccagATAACAGATGCAGTTGTTGTTGCAAGAATTCTTAATGCTACACTAGTTGTACCTGAGTTGGATCATCAATCTTTTTGGAAAGATGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - -ctttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -taaacaag