Sequence
atgc intronic sequence ATGC exonic sequencegtaaggcgctctctcatacacactccatgtggctagtgttgcatgttttatctctctgatcagtgtttctcagatgttattgtgtgtgtgttcagGTTTTGAAGGAGACGCTGCTTAGACATGGCTTCACCTTTGAATCTGAAACTGACACCGAGGTCATCCCCAAGCTTGCCAAGTTTGTCCACGACAAGGCGA
Basic information
species | Glycine max |
transcript | GLYMA18G47860.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47860.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g03900.1 (Oryza sativa), 3'ss of exon 2
------gtaaggcgctctctcatacacactccatgtg--gctagtgttgcatgttttatctctctgatcagtgtttctcagatgttattg-tgtgtgtgttcagGTTTTGAAGGAGACGCTGCTTAGACATGGCTTCACCTTTGAATCTGAAACTGACACCGAGGTCATCCCCAAGCTTGCCAAGTTTGTCCACGACAAGGCGA
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aacctcatgataccttctcaaattaatgtagcaacagatgataatgatgtaaacagataaattcccatcataactt----ggtatttttgatgtatctgctcagGTTCTGAAAGAGACACTAATCCGACATGGGTTCACCTTTGAGTCTGATACTGACACAGAAGTCATCCCTAAGTTGGCAAAGTTTGTTTTTGATAAGGCAC
upper sequence: GLYMA18G47860.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G005849_T03 (Zea mays), 3'ss of exon 1
----gtaaggcgctctctcatacacactccatgtggc-tagtgttgcatgttttatctctctga-tcagtgtttctcagatgttattgtgtgtgtgttcagGTTTTGAAGGAGACGCTGCTTAGACATGGCTTCACCTTTGAATCTGAAACTGACACCGAGGTCATCCCCAAGCTTGCCAAGTTTGTCCACGACAAGGCGA
| || | || || | | | | | | ||| | | | |||||| |||| | || | ||||||||| ||||| ||||| || ||| || |||||||||||||| ||||| || ||||| || |||||||| ||||| || ||||| || || || |
atcctcttgattctgttgtgaactaacgtggcaccatattatacttggtaaatgacaagtctaacttgatttttctctcatgtctgt-tgattctgttcagGTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACAGACACAGAAGTCATCCCTAAGCTAGCAAAGTTCGTTTTTGATAAATCTC
upper sequence: GLYMA18G47860.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ08214 (Selaginella moellendorffii), 3'ss of exon 2
gtaaggcgctctctcatacacactccatgtggctagtgttgcatgttttatctctctgatcagtgtttctcagatgttattgtgtgtgtgttcagGTTTTGAAGGAGACGCTGCTTAGACATGGCTTCACCTTTGAATCTGAAACTGACACCGAGGTCATCCCCAAGCTTGCCAAGTTTGTCCACGACAAGGCGA
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----------------------------------------gtct-ctctgcctttctcatgtgtttctctccctcgtaacctcctccattttcagGTGCTGAAAGAAACGCTGCTGCGCCACGGTTTTGAATTCGAGTCCGAGACTGATACCGAGGTCATTCCCAAGCTTGCCAAGTTCGTGCACGACAGGCTGT
upper sequence: GLYMA18G47860.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ12208 (Selaginella moellendorffii), 3'ss of exon 2
gtaaggcgctctctcatacacactccatgtggctagtgttgcatgttttatctctctgatcagtgtttctcagatgttattgtgtgtgtgttcagGTTTTGAAGGAGACGCTGCTTAGACATGGCTTCACCTTTGAATCTGAAACTGACACCGAGGTCATCCCCAAGCTTGCCAAGTTTGTCCACGACAAGGCGA
| | | | || ||| || | | |||| | | | | ||||||| |||| || |||||||| | || ||||| || || || || ||||| ||||||||||| ||||||||||||||||| || ||||||| | |
----------------------------------------gtct-ctctgcctttctcatgtggttctctc---cctaacctcctccattttcagGTGCTGAAAGAAACGCTGCTGCGCCACGGCTTTGAATTCGAGTCCGAGACTGATACCGAGGTCATTCCCAAGCTTGCCAAGTTCGTGCACGACAGGTTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatgttttatctctctgatcagtgtttctcagatgttattgtgtgtgtgttcagGTTTTGAAGGAGACGCTGCTTAGACATGGCTTCACCTTTGAATCTGAAACTGACACCGAGGTCATCCCCAAGCTTGCCAAGTTTGTCCACGACAAGGCGA
ctctgat putative branch site (score: 4)
ttttatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggcgctctctcatacacactccatgtggctagtgttgcatgttttatctctctgatcagtgtttctcagatgttattgtgtgtgtgttcagGTTTTGAAGGAGACGCTGCTTAGACATGGCTTCACCTTTGAATCTGAAACTGACACCGAGGTCATCCCCAAGCTTGCCAAGTTTGTCCACGACAAGGCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT