Sequence
atgc intronic sequence ATGC exonic sequence...gagtaatctgattttcttgtcttttcacttgaggttctgaaaaacttctgcgtttctttgtcttgtaattaaacatatggctgctacttgtgcacaacagGTGGGTGGCAGCTCAAAGCATATTTTATCATCTGTACAATCAAGTGTCGTACATGTCTCTGGATGAGATCTCTCCCTTGACATTTAGCATTGGAAACACC
Basic information
species | Glycine max |
transcript | GLYMA02G45840.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G45840.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 3'ss of exon 4
--gagta-atctgatt-ttcttgtcttttcacttgaggttctgaaaaacttctgcgtttctttgtcttgtaattaaacatatggctgctacttgtgcacaacagGTGGGTGGCAGCTCAAAGCATATTTTATCATCTGTACAATCAAGTGTCGTACATGTCTCTGGATGAGATCTCTCCCTTGACATTTAGCATTGGAAACACC
| | || |||| || | | || | | | || |||| | ||| ||| | || ||||| | || | | ||| | |||||||| || || || ||| | || || || | ||||| || ||||| |||||||||||||||||||| ||||| ||||||||||||||||| || ||
tatattgtatttgatgatttacaacatactacagcgtatgcagcaacacttgagtattttattgatat-tacttaaattttggg--gatg-ttgaatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTACATGTCTCTGGATGAGATTTCTCCATTGACATTTAGCATTGGCAATACG
upper sequence: GLYMA02G45840.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G431314_T01 (Zea mays), 3'ss of exon 4
gagtaat-ctgattttcttgtcttttcacttgaggttctgaaaaacttctgcgtttctttgtcttgtaattaaacatatggc-tgctacttgtgcaca-acagGTGGGTGGCAGCTCAAAGCATATTTTATCATCTGTACAATCAAGTGTCGTACATGTCTCTGGATGAGATCTCTCCCTTGACATTTAGCATTGGAAACACC
|| | ||| || ||| | | | | || | | || | | || ||| | | || | | || |||| | | | |||||| | || || || ||| | || ||||| | || || || ||||| ||||||||||| ||| |||||||||| ||||| ||||||||||| || ||
---tagtgctgcccttattgaggacttatatattatgttggattaattttatgattgcatgtatattgatattttccctaacgtgttactgtcgaatttatagGTGGATCGCTGCACAGAGCGTGTTCTATCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATCTCTCCATTGACGTTTAGCATTGGCAATACA
upper sequence: GLYMA02G45840.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
gagtaatctgattttcttgtcttttcacttgaggttctgaaaaacttctgcgtttctttgtcttgtaattaaacatatggctgctacttgtgcaca-acagGTGGGTGGCAGCTCAAAGCATATTTTATCATCTGTACAATCAAGTGTCGTACATGTCTCTGGATGAGATCTCTCCCTTGACATTTAGCATTGGAAACACC
| || | || || | | || ||| | | | | | | | | | | || ||| | || | || |||| || | | |||||| | || || || ||| | || || || | || || || ||||| ||||||||||| ||| |||| ||||| |||||||| |||||||| || ||
tattattttggattgatgttaggatctaatgatagtgatattatatcacgactgtatgtatactgatattttccctaatg-tgttactgttgaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
upper sequence: GLYMA02G45840.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 3
gagtaatctgattttcttgtcttttcacttgaggttctgaaaaacttctgcgtt--tctttgtcttgtaattaaacatatggctgctacttgtgcacaacagGTGGGTGGCAGCTCAAAGCATATTTTATCATCTGTACAATCAAGTGTCGTACATGTCTCTGGATGAGATCTCTCCCTTGACATTTAGCATTGGAAACACC
| ||| |||| | | ||| | ||| | || |||| | || | | |||||| || |||| || ||||||||||| || || || |||| ||||| || |||||||| ||||| |||||||| ||||||||||||||||||||||| ||||||||||||||||||
--attccctgtgtttcccactcagttgtaagtggtagttgttttctttttgcttggcttttgctaaggaaatgtttgtgtggctgttatttgtacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATACATGTCGCTGGATGAGATCTCTCCCTTGACGTTTAGCATTGGAAACACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgcgtttctttgtcttgtaattaaacatatggctgctacttgtgcacaacagGTGGGTGGCAGCTCAAAGCATATTTTATCATCTGTACAATCAAGTGTCGTACATGTCTCTGGATGAGATCTCTCCCTTGACATTTAGCATTGGAAACACC
ttgtaattaaacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagtaatctgattttcttgtcttttcacttgaggttctgaaaaacttctgcgtttctttgtcttgtaattaaacatatggctgctacttgtgcacaacagGTGGGTGGCAGCTCAAAGCATATTTTATCATCTGTACAATCAAGTGTCGTACATGTCTCTGGATGAGATCTCTCCCTTGACATTTAGCATTGGAAACACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - -cacttga
- - - - - - - - - - - - - - - - ggttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctac