Sequence
atgc intronic sequence ATGC exonic sequence...atattcagcatactattttctctgattcaatgtgctgctgctctacatgtgttctttgaataaaatcttcagctaactgtgttctttcccttctctccagTCCTTCCATTATTGCAAGTATAGGCGTGATGAAAACCAACTTTACATATTTGCTGATGATTGTGTTCCAAGGTGGCTTACTGCATCATACCACATAGATT
Basic information
species | Glycine max |
transcript | GLYMA20G38460.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38460.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g04480.1 (Oryza sativa), 3'ss of exon 1
atattcagcatactattttctctgattcaatgtgctgc-tgctctacatgtgttctttgaata--aaatcttcagctaactgtgttctttcccttctctccagTCCTTCCATTATTGCAAGTATAGGCGTGATGAAAACCAACTTTACATATTTGCTGATGATTGTGTTCCAAGGTGGCTTACTGCATCATACCACATAGATT
|| | ||| ||| | | || ||| | | | | | | || || |||| | |||| | | | | | | || | || ||||| || |||||||||||||| || | |||||||||||||| ||||| || ||||||||| ||||||| |||||||| || ||| || | ||||||||||
--tttaaatatagtatagtatac-atataatattcaccatatttcatataccttttttgtttgacaaatttctaacatttctttgtggtgccatctcctgcagTCATTTCATTATTGCAAGTACAGAAGGGATGAAAACCAACTGTACATCTTCGCTGATGATAGTGTTCCCAGGTGGCTCACAGCAGCAAATCACATAGATT
upper sequence: GLYMA20G38460.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G096972_T01 (Zea mays), 3'ss of exon 1
atattcagca--tactattttctctgattcaatgtgctgctgctctacatgtgttctttgaataaaatcttcagctaactgt--gttctttcccttctctccagTCCTTCCATTATTGCAAGTATAGGCGTGATGAAAACCAACTTTACATATTTGCTGATGATTGTGTTCCAAGGTGGCTTACTGCATCATACCACATAGATT
| || || ||| | | ||||| | || | | || || || ||| || | | ||| || |||| | | | | | ||||| || || ||||||||||| || || |||||||||||||| || |||||||||||||| ||||||| ||||||||||| || || | ||||||||||
-tgttgtacaattacctctattgttgattgactgagatccttacct---tggcttccttcctttatttctgatactttctgtttggtgccattttcttttgcagTCATTTCACTATTGCAAGTACAGACGAGATGAAAACCAACTCTATATATTTGCTGATGACAGTGTTCCCAGGTGGCTTACAACAGCACAACACATAGATT
upper sequence: GLYMA20G38460.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G55200.1 (Arabidopsis thaliana), 3'ss of exon 1
atattcagcatactattttctctgattcaatgtgct-gctgctctacatgtgttctttgaataaaatcttcagctaactgtgttctttcccttctctccagTCCTTCCATTATTGCAAGTATAGGCGTGATGAAAACCAACTTTACATATTTGCTGATGATTGTGTTCCAAGGTGGCTTACTGCATCATACCACATAGATT
| | | | |||| || || | | | || || || | | | ||| | ||| ||| || | | | || | || | ||||| |||||||| |||||||| ||||| || || || || || ||||||||||| ||||| || || || |||||||| || ||||| |||| | ||||
gtgagtggtagatcctttttcct-atatattttacttactactgtgtgctt-tgttttatagaaatatctcatgtagccttttcattatcgtttt--gcagTCTTTCCATTACTGCAAGTACAGGCGCGACGAGAATCAGCTGTACATATTTGCGGATGACTGCGTGCCGAGGTGGCTGACAGCATCGCACCATGTGGATT
upper sequence: GLYMA20G38460.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0317g00100.t01 (Vitis vinifera), 3'ss of exon 1
-------atattcagcatactattttctctgattcaatgtgctgctgctctacatgtgttctttgaataaaatcttcagctaactgtgttctttcccttctctccagTCCTTCCATTATTGCAAGTATAGGCGTGATGAAAACCAACTTTACATATTTGCTGATGATTGTGTTCCAAGGTGGCTTACTGCATCATACCACATAGATT
|| | ||||| ||| | | || | | | | | || | | || ||| || | || | | | | | ||||| |||||||||||||||||||| || |||||||| ||||| || ||||||||||||||| |||||||||| ||| | || ||||| |||||||||||||
aagtgagatgctt-gcataggcctttgttttatccctttcattagtacactt----ttcccctttaatgaacttactgactg--taaatcttgatgtcattttgcagTCATTCCATTATTGCAAGTATAGACGGGATGAAAATCAACTGTATATATTTGCTGATGATAGTGTTCCAAGATGGTTGACAGCATCTTACCACATAGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgtgttctttgaataaaatcttcagctaactgtgttctttcccttctctccagTCCTTCCATTATTGCAAGTATAGGCGTGATGAAAACCAACTTTACATATTTGCTGATGATTGTGTTCCAAGGTGGCTTACTGCATCATACCACATAGATT
agctaac putative branch site (score: 2)
ctgtgttctttccctt CT-rich tract
ttctttgaataaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atattcagcatactattttctctgattcaatgtgctgctgctctacatgtgttctttgaataaaatcttcagctaactgtgttctttcccttctctccagTCCTTCCATTATTGCAAGTATAGGCGTGATGAAAACCAACTTTACATATTTGCTGATGATTGTGTTCCAAGGTGGCTTACTGCATCATACCACATAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - -gcatact
- - - - - - - - - - -ctgattc
- - - - - - - - - - - - - - - - - ctgctgc
- - - - - - - - - - - - - - - - - - - - - - - -tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcagc