Sequence
atgc intronic sequence ATGC exonic sequence...ttaaaatggctcaatgttcatagcttctgtttgtgttgtaccttaattagtatttgcttttggattatattcccttctaagttacatccctctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCCGAGCAG
Basic information
species | Glycine max |
transcript | GLYMA18G02960.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 2
------------ttaaaatggctcaatgttcatagcttctgtttgtgttgtaccttaattagtatttgcttttggattatattcccttctaagttacatccctctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCCGAGCAG
|| || || |||| | |||| | || || || | || | || ||| ||| | | || || | || ||||||| | | |||||| ||||| ||||| ||||| || |||||||||||| ||||||||| ||||||| |||||||||| ||||||
gtacttgattttttcctttgatctaaaacccataa---cggtttcctcgaattcgtagttcataatccacttatcttgatgttcactttttacttcaatattt---atgtagCTCAAGTTCCAGGAACTACTCAGGATCATCTACAGATATTTAACATTGAAGCCAAAGCAAAGTTGAAATCACATCAGATGCCTGAGCAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 2
ttaaaatggctcaatgttcatagcttctgtttgtgttgtaccttaattagtatttgcttttggattatattcc--cttctaagttacatccctctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCCGAGCAG
| | | | | | | || | ||| | || | |||||| |||| || ||| || | |||| | | ||| ||||||||||||| | ||||| || || |||||| | ||||| ||||| ||||| |||||||| || |||||||| ||||| ||||| ||||||
--attgtcatttagtagtttcattggtggtctatgtgtcaatttcaaagttatttgtttttcatatactttctggctcatgagtttaaacattcttttgaagCTCAACTTCCGGGAACCACCCAGGATCACTTGCAAATATTTAATATTGAGATGAAAGCCAAAATGAAATCATATCAAATGCCTGAGCAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 3'ss of exon 2
ttaaaatggctcaatgttcatagcttctgtttgtgttgtaccttaattagtatttgcttttggattatattcccttctaagttacatccctctcttgaagCTCAACTCCAA-----GGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCCGAGCAG
|| || ||| || || | ||| | | | | ||| | || | | || || | | | ||| | || | | ||| | | | || |||| |||||||| || |||||||| ||||| ||| ||||||| ||||||||||| ||||| ||||| || |||
---taacagcgtcctgtccacc-ctcacatatgtttctatcgtcatttaattttcgactgaagagtacgtagtacta-acgttgcgccctgtccgcgtgaatcagCCCTGATACCTGGTTCAACACAAGATCATCTCCAAATTTTCAACATCGAATTGAAAGCCAAGATGAAATCGTATCAAATGCCAGAACAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 2
ttaaaatggctcaatgttcatagcttctgtttgtgttgtaccttaattagtatttgcttttggatt----atattcccttctaagttacatccctctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCCGAGCAG
||| | ||||| || | | || | | || | | || | | | | || | | | || | | | ||| | | || | || ||||| || || ||||| |||||||| ||| | ||||| ||||||||||| ||||| ||||| ||||||
----aatatattctagttcagcctttgtatatgattctggctttggatgatgttgaatcacgaaatcttagtactaatgtttgtgtcttgtttatgtgaaccagCCTTGATACCTGGTTCGACACAAGACCATCTCCAAATCTTTAACATCGAATTAAAAGCTAAGATGAAATCGTATCAAATGCCAGAGCAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 2
ttaaaatggctcaatgttcatagcttctgtttgtgttgtaccttaattagtatttgcttttggattatattcccttctaagttacatccctctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCCGAGCAG
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--------------------------------gtatgacatttca-ttttcgcgtgatcc-ggaggatacaactt----aactggtttgctcgtacgcagCTCAAATTCCTGGCACGAGCCAGGATCATCTCCAGATTTTTAACATAGAAATGAAGGCTAAGATGAAATCTCATCAAATGTCGGAACAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 2
ttaaaatggctcaatgttcatagcttctgtttgtgttgtaccttaattagtatttgcttttggattatattcccttctaagttacatccctctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCCGAGCAG
|| | | | | || || | ||| ||| | | | | | ||| | ||||||| | | || || | || ||||| || || ||||||||||| |||||||| || |||||||||||| |||| ||| | || |||
--------------------------------gtatgacatttca-ttctcgcgtgatcc-ggaggatacaactt----aactggtttgctcgtacgcagCTCAAATTCCTGGCACGAGCCAGGATCATCTCCAGATTTTTAACATAGAAATGAAGGCTAAGATGAAATCTCATCAAATGTCGGAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attagtatttgcttttggattatattcccttctaagttacatccctctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCCGAGCAG
ccttaat putative branch site (score: 4)
ttacatccctctctt putative PPT
ttttggattatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaaaatggctcaatgttcatagcttctgtttgtgttgtaccttaattagtatttgcttttggattatattcccttctaagttacatccctctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCCGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - -caatgtt
- - - - - - - - - - - gcttctg
- - - - - - - - - - - - - - - - -tgttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatccc