Sequence
atgc intronic sequence ATGC exonic sequence...tttttcatgtttttttatgacttttagattaaaattcggttagtcatactcttttattaattattgatatttttttcttgtcatttttttttttactcagATGGTCTAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAAAAATCATTGGAACACACACATAAAGAAAAAGCTCAAGAAAATGGGCATT
Basic information
species | Glycine max |
transcript | GLYMA02G41180.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G41180.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g33150.1 (Oryza sativa), 3'ss of exon 2
--tttttcatgtttttttatgacttttagattaaaattcggttagtcatactcttttattaattattgatatttttttcttgtcatttttttttttac------tcagATGGTCTAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAAAAATCATTGGAACACACACATAAAGAAAAAGCTCAAGAAAATGGGCATT
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gtacgataacattgtcctcgacacgttgggacaacatgc--ctgaacgta-tgataaattagtttttta-atgtatatataaccatttttatatacaaaacatgttagGTGGTCTAAGATTGCGTCTCATTTGCCTGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACTCACATCAAGAAGAAGCTCAAGAAAATGGGGATC
upper sequence: GLYMA02G41180.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G16600.1 (Arabidopsis thaliana), 3'ss of exon 2
tttttcatgttttttta-tgacttttagattaaaat--tcggttagtcatactcttttattaattattgatatttttttcttgtcatttttttttttactcagATGGTCTAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAAAAATCATTGGAACACACACATAAAGAAAAAGCTCAAGAAAATGGGCATT
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tagttggtctgatgaaaatgactgaacagtcgaaatatttactaaattttaagcttatatgattt--tga-atctttaacttttattttgtgtgtgtgtgcagATGGTCAAAGATTGCCTCTCATCTACCAGGAAGAACTGATAATGAAATAAAGAACCATTGGAACACACACATAAAGAAAAAGCTAAGGAAAATGGGTATT
upper sequence: GLYMA02G41180.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0006g00450.t01 (Vitis vinifera), 3'ss of exon 2
tttttcatgtttttttatgacttttagattaaaattcggttagtcatactcttttattaatt---attgatatttttttcttgtcatttttttttttactcagATGGTCTAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAAAAATCATTGGAACACACACATAAAGAAAAAGCTCAAGAAAATGGGCATT
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ttccttttttttgtccctgaaattaattccaaaacatatccatgtgaaattcttcttcaattttaatttatatgtttgttttttcaacgtggattt---gcagATGGTCCAAGATTGCTTCTCATCTACCAGGAAGAACCGATAACGAAATCAAGAACCATTGGAATACCCACATCAAGAAAAAACTTAAAAAGATGGGTATTMapped 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|192296205|gb|FG989041.1|FG989041EST: GAATACGAAGAAAAAATGGTCATTGATCTTCATGCTCAACTTGGCAATAG ATGGTCTAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAA
genomic: GAATACGAAGAAAAAATGGTCATTGATCTTCATGCTCAACTTGGCAATAGgttatttcct ... ttttactcagATGGTCTAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAA
EST:
gi|23728665|gb|BU762393.1|BU762393EST: GAATACGAAGAAAAAATGGTCATTGATCTTCATGCTCAACTTGGCAATAG ATGGTCTAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAA
genomic: GAATACGAAGAAAAAATGGTCATTGATCTTCATGCTCAACTTGGCAATAGgttatttcct ... ttttactcagATGGTCTAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atactcttttattaattattgatatttttttcttgtcatttttttttttactcagATGGTCTAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAAAAATCATTGGAACACACACATAAAGAAAAAGCTCAAGAAAATGGGCATT
tatttttttcttgtca CT-rich tract
ttttattaattattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttcatgtttttttatgacttttagattaaaattcggttagtcatactcttttattaattattgatatttttttcttgtcatttttttttttactcagATGGTCTAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAAAAATCATTGGAACACACACATAAAGAAAAAGCTCAAGAAAATGGGCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - tcatgtt
- - - - - - - - - - - - - - - - - - - - - - catactc