Sequence
atgc intronic sequence ATGC exonic sequence...aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
Basic information
species | Glycine max |
transcript | GLYMA20G39050.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g48820.2 (Oryza sativa), 3'ss of exon 4
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaatt-ttaaatggtatttg-ttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
|||||| | | || | || ||| || | | ||| | | || ||| | ||||| |||| | |||| | || |||||||||| ||||||||||||||||||||||||||| |||| || ||
-------------gtgacattttagttccgtttctt---ttcgtatacaatgtcacttaatcttgtgtgattaatttcatattgtattttggcatgcaatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattt-taaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
|||| | | ||| | |||| || ||| || || || ||| | |||| | | ||| | | ||| ||| ||| | || || | || |||||||||| ||||||||||| ||||||||||||||| ||||||| ||
-------gtgttaatt-tatctcctatttc-ttgtgcagt-gctacttatcctttcttaatgatggtatttagg-aagtat--gtttgttattc--tgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG
upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G361847_T04 (Zea mays), 3'ss of exon 3
aaaacaa-atgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
|| | || || || | | | || || |||| |||| | | || || |||| || | ||| |||| |||| | ||| |||| | ||| ||||||| || ||||||||||||||||||||||||||| |||| || ||
gtaatatcgtggttcctttttctcaagttc--ttat----ttaacctt----gtattgcttgttattaattgc---atttttgaattttca--tatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G056099_T02 (Zea mays), 3'ss of exon 3
aaaacaaatgtttactctattttaaatttggttatgcggtt-aatatctaaaatt-ttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
| || | | | | | || | | | | || | | | | | || | | | || | ||| || |||| || | || || | | ||| ||||||| || ||||||||||||||||||||||| ||| |||| || ||
-------gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattcttt--agGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG
upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G174284_T01 (Zea mays), 3'ss of exon 4
aaaacaaatgtttactctattttaaat-ttggttatgcggtt-aatatctaaaatt-ttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
|||| | ||| | | || | | | | || | | | | | || | | | | | ||| || |||| || | || || | | ||| ||||||| || ||||||||||||||||| ||||||||| |||| || ||
---------gttt-ttttatctcatatgtcttctgtactctttagtgtttgttaccatttcacaatgatggaatctagataatgcatttgatattcttt--agGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGGAAAAGTCGGCTGAGGAAAAAG
upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G12250.5 (Arabidopsis thaliana), 3'ss of exon 4
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattat----tgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
|| || | | || | || |||| | | | ||| | | || || | |||| || | |||| || || ||||||||||| ||||||||||||||||||||||| | ||||| |||||
-------------gtgatagattcatctctgtggatcaactagcatctgtgtatattacgcatatgcataatctgttttgtttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG
upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G06950.3 (Arabidopsis thaliana), 3'ss of exon 4
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
| |||| | | || || | | | | ||| ||| | || | || | | || || | || |||| || ||||||| || ||||||||||| || |||||||||||||| ||||| | ||||| |||||
--gtgacatgtccatctc--tgtagataagatca--ctgtttttattcag----ccaatttataatctctttttgtttccttatattttgatc--catagACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTGAGGAAGAAG
upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 6
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
| | || | ||| | || | | || |||| || | | ||| || | ||| || ||| | | |||||||| || ||||||||||| |||||||| || ||| ||||||| || ||||||||||||
-----------gtcatatagatcaaact-aattgcgtgtatatcatctcaa-ctgaatgcagtaacatttgatgatcttttgtttgtttgtatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|192300889|gb|FG992949.1|FG992949EST: CTGTGGCTTCTGACTCCAGTGACAGATCAAAGGATAAATCAGATCAGAAG ACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTG
genomic: CTGTGGTTTCTGACTCCAGTGACAGATCAAAGGATAAATCAGATCAGAAGgtaaagtgta ... attattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
ttttaat putative branch site (score: 3)
tatttgttacgtgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
-aaacaaa
- - - - - - - - - - - - - - - gttatgc