Sequence
atgc intronic sequence ATGC exonic sequence...tttattcctatgcttgttttatttctcttcatccctgttttttcccactcaatagttttctaataaaatcaagtaatgtctattatatcttttattgcagGAAAAGTGGTTGGAAGTTTTGGGGTGTGGAGTGACAGAGCAAGAGATTCTGAAGAGAAATGGGAAACCTAATAATGTTGCTTGGGCTTTTGGTCTAGGGT
Basic information
species | Glycine max |
transcript | GLYMA18G52890.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 7
lower sequence: AC211349.4_FGT001 (Zea mays), 3'ss of exon 5
-tttattcc-tatgcttgttttatttctcttcatccctgttttttcccactcaatagttt---tctaataaaatcaagtaatgtctattatatcttttattgc---agGAAAAGTGGTTGGAAGTTTTGGGGTGTGGAGTGACAGAGCAAGAGATTCTGAAGAGAAATGGGAAACCTAATAATGTTGCTTGGGCTTTTGGTCTAGGGT
| |||| | | | | | ||| | || || | | | | | || || | | | | || || | | || |||| | |||||||| ||||||||||||||||| || ||||| || ||| |||| |||||||| | | |||| |||||||| ||||| | || |
gtatattggatgtattcgactattttttttttatagtaacaagcccaaaacatgttgcataagtcacattggcatgaatgagtctgaataaatttctcatcttctaagGATGATTGGTTGGAGGTTTTGGGGTGTGGAGTCACCGAGCAGGAAATTTTGAAAAGAAATGGCAGGAGGGACCATGTGGCTTGGGCCTTTGGATTGGGCT
upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv19s0027g01470.t01 (Vitis vinifera), 3'ss of exon 5
-----tttattcctatgcttgttttatttctcttcatccctgttttttcccactcaatagttttctaataaaatcaagtaatgtctattatatcttttattgcagGAAAAGTGGTTGGAAGTTTTGGGGTGTGGAGTGACAGAGCAAGAGATTCTGAAGAGAAATGGGAAACCTAATAATGTTGCTTGGGCTTTTGGTCTAGGGT
||| | || ||| || | | | || | ||| | ||| || | | | || | ||| || || ||| || ||||| ||||| || |||||||||||||| || ||||| |||||||||||||| || | |||| || ||| ||
aatagttttgtatta-acttattatttgacaattattgcctatagttttttgg-cagaactgctacgatctcactaagcaacatccattg-ataatttat--cagGAGAACTGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTAAAGAAAAGTGGTAA-----------------------------------
upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 5
---tttattcctatgcttgttttatttctcttcatccctgttttttcccactcaatagttttctaataaaatcaagtaatgtctattatatcttttattgcagGAAAAGTGGTTGGAAGTTTTGGGGTGTGGAGTGACAGAGCAAGAGATTCTGAAGAGAAATGGGAAACCTAATAATGTTGCTTGGGCTTTTGGTCTAGGGT
||| | | ||| || | | || | ||| | ||| | | | | || | | | || || ||| | ||| | ||||| || |||||||||||||| || ||||| |||||||||||||| || | |||| || ||| ||| | |||||||||||||||||||||| || || |
atatttttgtatcaacttattacttgacaattattgcctatagttttttttgtggaactgctatgatctcactatgcaacatccattg-gtaatttgt--cagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTAAAGAAAAGTGGTAAAACAGATAATGTTGCTTGGGCTTTTGGGCTTGGAT
upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 3'ss of exon 6
-tttattcctatgcttgttttatttctcttcatccctgtttt--ttcccactcaatagttttctaataaaatcaagtaatgtctattatatcttttattgcagGAAAAGTGGTTGGAAGTTTTGGGGTGTGGAGTGACAGAGCAAGAGATTCTGAAGAGAAATGGGAAACCTAATAATGTTGCTTGGGCTTTTGGTCTAGGGT
|| | | | | || | | | || || | || | | | | | || | ||| || || ||| || ||||| ||||| || |||||||||||||| || ||||| |||||||||||||| || | |||| || ||||||| | ||||||||||||||||||||| || || |
gaatagttttgtattaacttattatttgacaattattgccatagttttttggcggaactgctatgatctcactaagcaacatccattg-ataatttat--cagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTAAAGAAAAGTGGGAAAACAGGTAATGTTGCTTGGGCTTTTGGGCTTGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactcaatagttttctaataaaatcaagtaatgtctattatatcttttattgcagGAAAAGTGGTTGGAAGTTTTGGGGTGTGGAGTGACAGAGCAAGAGATTCTGAAGAGAAATGGGAAACCTAATAATGTTGCTTGGGCTTTTGGTCTAGGGT
ttctaat putative branch site (score: 2)
tcttttatt putative PPT
taataaaatcaagtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttattcctatgcttgttttatttctcttcatccctgttttttcccactcaatagttttctaataaaatcaagtaatgtctattatatcttttattgcagGAAAAGTGGTTGGAAGTTTTGGGGTGTGGAGTGACAGAGCAAGAGATTCTGAAGAGAAATGGGAAACCTAATAATGTTGCTTGGGCTTTTGGTCTAGGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - cctatgc
- - - - - - - - - - - - ctcttca
- - - - - - - - - - - - - - - - ccctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaaa