Sequence
atgc intronic sequence ATGC exonic sequence...ctggtcatttgtgattgctgccaagtcaaaaccaatcactttcttcatcaaatgtttaacattaaatcattaattaactactgggttttaatttttacagGTGGGTAGCTGCCCAGAGTGTCTTCTACCATCTGTACAATCAAGTCTCTTACATGTCTCTTGATCAGATTTCTCCCTTAACATTCAGCATAGGGAACACA
Basic information
species | Glycine max |
transcript | GLYMA17G01890.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G01890.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 3'ss of exon 4
ctggtcatttgtgattgctgccaagtcaaaaccaatcac--tttcttcatcaaatgtttaacattaaat---cattaattaactactggg--ttttaatttttacagGTGGGTAGCTGCCCAGAGTGTCTTCTACCATCTGTACAATCAAGTCTCTTACATGTCTCTTGATCAGATTTCTCCCTTAACATTCAGCATAGGGAACACA
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-------tatattgtatttgatgatttacaacatactacagcgtatgcagcaacacttgagtattttattgatattacttaaattttggggatgttgaatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTACATGTCTCTGGATGAGATTTCTCCATTGACATTTAGCATTGGCAATACG
upper sequence: GLYMA17G01890.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
ctggtcatttgtgattgctgccaag--tcaaaaccaatcactttcttcatcaaatgttta-acattaaatcattaattaactactgggttttaatttttacagGTGGGTAGCTGCCCAGAGTGTCTTCTACCATCTGTACAATCAAGTCTCTTACATGTCTCTTGATCAGATTTCTCCCTTAACATTCAGCATAGGGAACACA
| |||| ||||| || | | || | | | || | | | ||| | | | | | || ||| | | || | ||| | |||||| | ||||| ||||| || |||||||| | || || || || || ||||||||||| |||||||||||||| || ||||||||||| || || |||
--tattattttggattgatgttaggatctaatgatagtgatattatatcacgactgtatgtatactgatattttccctaatgtgttactgttgaattt-atagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
upper sequence: GLYMA17G01890.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 3
ctggtcatttgtgattgctgccaagtcaaaaccaatcactttcttcatcaaatgtttaacattaaatcatt-aattaactactgggttttaatt---tttacagGTGGGTAGCTGCCCAGAGTGTCTTCTACCATCTGTACAATCAAGTCTCTTACATGTCTCTTGATCAGATTTCTCCCTTAACATTCAGCATAGGGAACACA
|| | ||| || | || |||| | || || ||| | |||| | | || ||| | | |||||| ||| ||||||||| | ||| |||||||| ||||| || || ||||| ||||| |||||||||||| | || || || |||||||| || || || | || |||||
ctaaacgtttaagaatcct--tgagtctt--tttagtgattagggcaatgaatccatcccattcacttatccgattccacatttttctttaatcaaatttgcagGTGGGTGGTTGCGCAGAGTGTGTTCTATCACCTCTACAACCAAGTGTCTTACATGTCTTTAGACCAAATCTCTCCCTTGACGTTTAGTGTTGGTAACACC
upper sequence: GLYMA17G01890.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 3
ctggtcatttgtgattgctgccaagtcaaaaccaatcactttcttcatcaaatgtttaacattaaatcattaattaactactgggttttaatttttaca-----gGTGGGTAGCTGCCCAGAGTGTCTTCTACCATCTGTACAATCAAGTCTCTTACATGTCTCTTGATCAGATTTCTCCCTTAACATTCAGCATAGGGAACACA
| |||| || | | ||| || | | | ||| | || || | || | | || | | || | | |||| |||| ||||||| || ||||||||||| ||||| || || |||||||| || || |||||||| || ||| |||| |||||||| || || ||||| || |||||
---attccctgtgtttcccactcagttgtaagtggtagttgttttctttt--tgcttggcttttgctaaggaaatgtttgtgtggctgttatttgtacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATACATGTCGCTGGATGAGATCTCTCCCTTGACGTTTAGCATTGGAAACACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcaaatgtttaacattaaatcattaattaactactgggttttaatttttacagGTGGGTAGCTGCCCAGAGTGTCTTCTACCATCTGTACAATCAAGTCTCTTACATGTCTCTTGATCAGATTTCTCCCTTAACATTCAGCATAGGGAACACA
tttttac CT-rich tract
aatgtttaacattaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctggtcatttgtgattgctgccaagtcaaaaccaatcactttcttcatcaaatgtttaacattaaatcattaattaactactgggttttaatttttacagGTGGGTAGCTGCCCAGAGTGTCTTCTACCATCTGTACAATCAAGTCTCTTACATGTCTCTTGATCAGATTTCTCCCTTAACATTCAGCATAGGGAACACA
- - - - - - - ttgctgc
- - - - - - - - - - - - - caaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actactg