Sequence
atgc intronic sequence ATGC exonic sequence...ttaagagaatttgttgcttctgccatctgaaattgaaactgggggtcttgtcctttgtgggatcaatgcgtgtacctaatgtgtttattttgttttgcagTGGCCACTCCTAAACAGATTAGAGAACTGATGCAGGTGGAAGGCCTTACAAATGATGAAGTGAAAAGCCATTTGCAA
Basic information
species | Glycine max |
transcript | GLYMA11G06230.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G06230.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g39640.1 (Oryza sativa), 3'ss of exon 3
--ttaagagaat-ttgttgcttctgccatctgaaattgaaactgggggtcttgtcctttgtgggatcaatgcgtgtacctaatgtgtttattttgttt-tgcagTGGCCACTCCTAAACAGATTAGAGAACTGATGCAGGTGGAAGGCCTTACAAATGATGAAGTGAAAAGCCATTTGCAA
|| | | |||||| || || | |||||| | || | || ||| | | || | | |||||| ||| | ||||| ||||| || ||||| || |||||||| || |||||| |||| || ||||| || ||||||||||| |||||||| ||||
atttgtggtcacattgttgattgctcctagtaaaattgtt-tgattaattttttgattggtgcgctgaa---acttgcttaatgtttttttattgttgatgcagCTGCAACTCCCAAGCAGATTAGGGAGCTGATGAAGGTTGATGGCCTCACTAATGATGAAGTCAAAAGCCACCTGCAG
upper sequence: GLYMA11G06230.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G171468_T02 (Zea mays), 3'ss of exon 3
------------------ttaagagaatttgttgcttctgccatctgaaattgaaactgggggtcttg-tcctttgtgggatcaatgcgtgtacctaatgtgtttattttgt--tttgcagTGGCCACTCCTAAACAGATTAGAGAACTGATGCAGGTGGAAGGCCTTACAAATGATGAAGTGAAAAGCCATTTGCAA
| ||| || | | | || | ||| | | || || || || | ||| ||| | || | | || ||||||||||| ||||| |||||||| || || ||||||| ||||| || |||||||| |||||||||||||||||| | ||
gtcagagtgtgagaccgatcgcctagctttaccgccattaatttgtccaaataaaaaaaagttccccactcgactgcaagagaaa-gtaagtat-taacgggtctctcatggaatttgcagTGGCTACTCCGAAACAGATCAGGGAGGTGATGCAAGTGGACGGGCTTACAAACGATGAAGTGAAAAGCCATCTCCAG
upper sequence: GLYMA11G06230.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G124540_T01 (Zea mays), 3'ss of exon 3
ttaagagaatttgttgcttctg-ccatctgaaattgaaactgggggtcttgtcctttgtgggatcaatgcgtgtacctaatgtgtttattttgttttgcagTGGCCACTCCTAAACAGATTAGAGAACTGATGCAGGTGGAAGGCCTTACAAATGATGAAGTGAAAAGCCATTTGCAA
|| | | | | | | |||| || ||| | | ||| | | ||| || || | ||| || | | ||||||| || ||||| || ||||| || || ||||| ||||||| || |||||||| |||||||||||||||||| | ||
gtacatatacacgacaccgcggatcgtctgtaa--gaagtttactactagttgcttgctagaggagatgtgt-taacgaat---ttcaccgttggttgcagTTGCTACTCCGAAGCAGATCAGGGAGGTGATGAAGGTGGACGGGCTTACAAACGATGAAGTGAAAAGCCATCTCCAG
upper sequence: GLYMA11G06230.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G173882_T01 (Zea mays), 3'ss of exon 3
----------------------------------------ttaagagaatttgttgcttctgccatctgaaattgaaactgggggtcttg--tcctttg---tgggatcaatgcgtgtaccta-atgtgtttattttgttttgcagTGGCCACTCCTAAACAGATTAGAGAACTGATGCAGGTGGAAGGCCTTACAAATGATGAAGTGAAAAGCCATTTGCAA
|| | || || | | | | | | | | || || | | | | ||| || || | || | | | || || | | | |||||| ||||| || || ||||| || || |||||| ||||||| ||||| ||||| || |||||||||||||| | ||
gtgagccttgctcttcagatgcaaattatttcttgccggttttgggcggcctgcagcgtgttcttacctacttgcttgcctgccgtattagatacgtagagttggaattaacgagttcattcatgtctgattgtct-gcactgcagTTGCCACCCCAAAGCAGATCAGGGAGCTGATGAAGGTGGACGGCCTCACAAACGACGAAGTGAAAAGCCACCTTCAG
upper sequence: GLYMA11G06230.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0197g00060.t01 (Vitis vinifera), 3'ss of exon 3
ttaagagaatt-tgttgcttctgccatctgaaattgaaactgggggtcttgtcctttg---tgggatcaatgcgtg-tac-ctaatgtgtttattttgttttgcagTGGCCACTCCTAAACAGATTAGAGAACTGATGCAGGTGGAAGGCCTTACAAATGATGAAGTGAAAAGCCATTTGCAA
||| || | || | || |||| || || | | | | ||| || || || | | | ||| || || | | || ||||| |||||||||||||||||| ||||||| ||||| |||||||| || || || |||||||| ||||||||||| ||
-----agatttctaatggaaaagttttcagaaaac-aatttgagatcatggatccttgaattgaattccatctgggacatgctactgaaattttccttttctgcagCAGCCACTCCTAAACAGATTCGAGAACTCATGCAAGTGGAAGGTCTCACTAACGATGAAGTAAAAAGCCATTTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgtcctttgtgggatcaatgcgtgtacctaatgtgtttattttgttttgcagTGGCCACTCCTAAACAGATTAGAGAACTGATGCAGGTGGAAGGCCTTACAAATGATGAAGTGAAAAGCCATTTGCAA
acctaat putative branch site (score: 3)
ttttgtttt putative PPT
taatgtgtttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaagagaatttgttgcttctgccatctgaaattgaaactgggggtcttgtcctttgtgggatcaatgcgtgtacctaatgtgtttattttgttttgcagTGGCCACTCCTAAACAGATTAGAGAACTGATGCAGGTGGAAGGCCTTACAAATGATGAAGTGAAAAGCCATTTGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - -tgttgct
- - - - - - - - - - tgccatc
- - - - - - - - - - - - - - - - - - - ctggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcgtgt