Sequence
atgc intronic sequence ATGC exonic sequence...gattgcaatagtctgccaactgtccgtgcttaaattttttgggcattttctagaagactttgaaggttgcttctaattactcatttttcttatgaaatagGCCGCCAAACTTTCCTGAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAGAGAGGCAGTGATGTTATTATTGTTCTTGTTGGGAACAAAACTGACCT
Basic information
species | Glycine max |
transcript | GLYMA01G41090.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G41090.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 3
gattgcaatagtctgccaactgtccgtgcttaaattttttgggcattttctagaagactttgaaggttgcttctaattactc---atttttctta--tgaaatagGCCGCCAAACTTTCCTGAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAGAGAGGCAGTGATGTTATTATTGTTCTTGTTGGGAACAAAACTGACCT
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----atgatt-tttaatagcaatgtcatttttaattcgttttgcattataaaagctctttcctatcctgcctcctttttccttaaatttgttttacatgctgtagGCAGACAGTCTTTCCTAAACACTTCAAAATGGATAGAGGAAGTTAGAACTGAGAGGGGCAGTGATGTTATCATTGTGCTGGTTGGGAACAAAACTGATCT
upper sequence: GLYMA01G41090.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G075719_T02 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------gat-tgcaatagt--ctgccaactgtccgtgcttaaattttttgggcattttctaga-agactttgaaggttgcttctaattactcatttttcttatgaaatagGCCGCCAAACTTTCCTGAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAGAGAGGCAGTGATGTTATTATTGTTCTTGTTGGGAACAAAACTGACCT
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gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT
upper sequence: GLYMA01G41090.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------gattgcaatagt--ctgccaactgtccgtgcttaaattttttgggcattttctaga-agactttgaaggttgcttctaattactcatttttcttatgaaatagGCCGCCAAACTTTCCTGAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAGAGAGGCAGTGATGTTATTATTGTTCTTGTTGGGAACAAAACTGACCT
| ||| | | || |||| ||||| ||| | | || | | | ||||| | || || | |||| ||| | | ||| ||||| | || | ||| | || ||||| |||||||| || || || |||| |||||| |||||||||||||| ||||| |||||||||||||||||||||||
gtaatctccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttactatt--ttgttcttacctttttgtttcatgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctagaagactttgaaggttgcttctaattactcatttttcttatgaaatagGCCGCCAAACTTTCCTGAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAGAGAGGCAGTGATGTTATTATTGTTCTTGTTGGGAACAAAACTGACCT
ttctaat putative branch site (score: 2)
ttactcatttttctt CT-rich tract
atttttcttatgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattgcaatagtctgccaactgtccgtgcttaaattttttgggcattttctagaagactttgaaggttgcttctaattactcatttttcttatgaaatagGCCGCCAAACTTTCCTGAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAGAGAGGCAGTGATGTTATTATTGTTCTTGTTGGGAACAAAACTGACCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
gattgca
- - - - - - ctgccaa
- - - - - - - - - - - tccgtgc
- - - - - - - - - - - - - - - - - - - - -ggcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gactttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttct