Sequence
atgc intronic sequence ATGC exonic sequence...actaaaatcctacattattgacatcaaccttttgagttaatctattgaaatttatcattgttatgatctaatagtgtttgctttatatgggaccttgaagGCTATTGCTGGAGAAGCTGGTGTTCCGTTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
Basic information
species | Glycine max |
transcript | GLYMA14G29780.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G29780.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 7
actaaaatcctacattattgacatcaaccttttgagttaatctatt----gaaatttatcattgttatgatctaatag--tgtttgctttatatgggaccttgaagGCTATTGCTGGAGAAGCTGGTGTTCCGTTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
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-----agacttactcaaagctcttttttttttctagttactcttttctccaacgttcatttccttcataagttcgtaccttactggagttaactttgtgcttta-gGCTATCGCTGGTGAAGCTGGTGTGCCATTTTTTTATCGGGCAGGTTCTGAATTTGAGGAAAT
upper sequence: GLYMA14G29780.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 7
actaaaatcctacattattgacatcaaccttttgagttaatctattgaaat-ttatcattgttatgatctaatagtgtttgctttatatgggaccttga---agGCTATTGCTGGAGAAGCTGGTGTTCCGTTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
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----ggacgccattgtgccatctccagctgttatcctatagtttttgtgctattgctgttgtcttgaccaaacataccttactggagctgtctttttgccccagGCCATTGCTGGAGAAGCTGGTGTACCATTCTTTTACCGAGCAGGCTCTGAATTTGAGGAAAT
upper sequence: GLYMA14G29780.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 7
actaaaatcctacattattgacatcaaccttttgagttaatctattgaaat-ttatcattgttatgatctaatagtgtttgctttatatgggaccttga---agGCTATTGCTGGAGAAGCTGGTGTTCCGTTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
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----atatgccattgtgccatctgcagctgttatcctatagtttttgtgctactgctgttgtcttgaccaaacataccttactggagctggctttttgctccagGCCATTGCTGGAGAAGCTGGCGTACCATTCTTTTACCGAGCAGGTTCTGAATTTGAGGAAAT
upper sequence: GLYMA14G29780.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------------------------actaaaatcctacattattg-----acatcaaccttttgagttaatctattgaaatttatcattgttatgatctaata-gtgtttgctttatatgg----gaccttgaagGCTATTGCTGGAGAAGCTGGTGTTCCGTTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
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gtaagttctcacatagttgttatattgtcgtctcttgttgaattggttattacttattatgagtgtgtgttttcacagtcatattccacttaataataaattcttattacgctaccaatattctgattgattttacaataagttaacacggtttaaattttgaagGCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTATAGAGCTGGATCTGAATTTGAAGAGAT
upper sequence: GLYMA14G29780.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 7
-----actaaaatc-ctacattattgacatcaaccttttgagttaatctattgaaatttatcattgttatgatctaatagtgtttgctttatatgggaccttgaagGCTATTGCTGGAGAAGCTGGTGTTCCGTTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
| ||| || || | | || | | |||| || |||||| || || |||| | | || | ||||| ||||| || || ||| || |||||||||||||||||||| ||||| || || ||||||||| ||||||| ||||||||||| || ||
tccgtattaatttctctgcccttttcatttttgtcttt-gatttaatcaat-gatattttttac-attctaatctatg---gtttgattcatttggaactttgaagGCTATTGCTGGAGAGGCTGGAGTACCATTTTTCTATAGAGCAGGTTCTGAATTTGAAGAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaatttatcattgttatgatctaatagtgtttgctttatatgggaccttgaagGCTATTGCTGGAGAAGCTGGTGTTCCGTTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
atctaat putative branch site (score: 3)
tttatcattgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actaaaatcctacattattgacatcaaccttttgagttaatctattgaaatttatcattgttatgatctaatagtgtttgctttatatgggaccttgaagGCTATTGCTGGAGAAGCTGGTGTTCCGTTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - -tcctaca
- - - - - - - - - - - atcaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttatg