Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtttgttcctttggtttacaaattgaggttgctgattgttgctgaaccttataaatttctcagaaatttatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTATTGTTCTCTT
Basic information
species | Glycine max |
transcript | GLYMA16G32890.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G32890.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os04g18010.1 (Oryza sativa), 3'ss of exon 21
--gtaatgtttgttcctttgg----tttacaaattgaggttgc---tgattgttg-ctgaaccttataaatttct---cagaaatttatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTATTGTTCTCTT
| | ||| | || | |||| || | | | | || ||| | | || ||| | | || ||| || || |||| | |||||||||||| | || |||||||| || || || |||||||| ||||||||||| | || |||||||| ||||| ||||||||| | || |||||||||
gcttgagatttatcttgtttgaaaatttaatgatcaaaggtacacatgtctgtaggtttaattatattattcactgaacagttatgcatttttacttcagAATACAACCACCAAGGAAAATGAGACCCTGTTGGCCATTGGGACTGCTTATGTTCTTGGGGAGGATGTAGCTGCTAGAGGACGTGTGCTTCTGTTCTCTT
upper sequence: GLYMA16G32890.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G453879_T02 (Zea mays), 3'ss of exon 6
gtaatgtttgttcctttggtttacaaattgaggttgctgattgttgctgaaccttataaatttctcagaa----atttatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTATTGTTCTCTT
| | | | ||| || || ||| | | || || || |||| ||||| ||| || || ||||| ||| | | || ||||||||||| || | |||||||| ||||||||||| ||||| |||||||||||||| |||||||| | || |||||||||
---gtatgtatgtcttctacacttgtatggatactgc--actcaaactaaaatttt---atttaccagaatattattgattttcgcctcagAACACATCTACGAAGGAAAATGAAACCCTGATGGCCATTGGAACTGCTTATGTTCAAGGGGAGGATGTTGCTGCTAGAGGACGGGTGCTTCTGTTCTCTT
upper sequence: GLYMA16G32890.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G453879_T01 (Zea mays), 3'ss of exon 6
gtaatgtttgttcctttggtttacaaattgaggttgctgattgttgctgaaccttataaatttctcagaa----atttatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTATTGTTCTCTT
| | | | ||| || || ||| | | || || || |||| ||||| ||| || || ||||| ||| | | || ||||||||||| || | |||||||| ||||||||||| ||||| |||||||||||||| ||
---gtatgtatgtcttctacacttgtatggatactgc--actcaaactaaaatttt---atttaccagAATATTATTGATTTTCGCCTCAGAACACATCTACGAAGGAAAATGAAACCCTGATGGCCATTGGAACTGCTTATGTTCAAGGGGAGGATGTTGCTGCTAG-----------------------
upper sequence: GLYMA16G32890.1 (Glycine max), 3'ss of exon 21
lower sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 21
------------gtaatgtttgttcctttggtttacaaattgaggttgctgatt--gttgctg-aaccttataaatttctcagaaatttatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTATTGTTCTCTT
||| | | || | || | ||| || |||| |||| | ||||| | | || |||||| ||| | || || |||||||||||| | || |||| ||||| ||||| ||||| ||||||||||||||||| || ||| | || | |||||||
gtaagttagctactaacccgcctaatgtcatatttggatcagatctctctgttttaattgcaataaccaagccacattctcttactccctggggtgtttcagAATGCAAGCACAGGGGAGAATGAAACACTTCTTGCTGTTGGGACTGCGTATGTCCAAGGGGAGGATGTTGCTGCAAGGGGCCGTGTGCTTCTTTTCTCTT
upper sequence: GLYMA16G32890.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv16s0022g01860.t01 (Vitis vinifera), 3'ss of exon 21
---------------------------------------------------------------------------------------------------------------gtaatgtttgttcctttggtttacaaattgag-gttgctgattgttgctgaaccttataaatt-tctcagaaatttatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTATTGTTCTCTT
| | || || ||| || ||| | || ||| ||| || |||| | || | |||| |||||||||| ||| |||||||||||||||||||||| |||||||| |||||||| || ||||| ||||||||||||||||| ||||| | || || || |||
gtgagttaattctttgccattccaactgtttctttgtgttttggttttggcttctttcttgaattctcgtcatgggagaggcgtgtggtgagtgttggggggggattagatatgttcttggtgaagctgggttggtgtttgtttaattcttatttctgcctgttctagaaaatcataattaccatgtgtcttacctgcagAATACTACCACAAAAGAAAATGAAACACTTTTGGCCATTGGGACTGCTTACGTACAAGGGGAGGATGTTGCTGCAAGGGGACGGGTGCTTTTATTTTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgctgattgttgctgaaccttataaatttctcagaaatttatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTATTGTTCTCTT
tgctgat putative branch site (score: 3)
tttatcttt putative PPT
ttataaatttctcaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtttgttcctttggtttacaaattgaggttgctgattgttgctgaaccttataaatttctcagaaatttatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTATTGTTCTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA