Sequence
atgc intronic sequence ATGC exonic sequence...tccaagtcttctgaaatccattccttgtaatctgcttataagttctaacaattttcagtttatcaaatataaatgtcttattgatattgccatctaacagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
Basic information
species | Glycine max |
transcript | GLYMA14G01920.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 10
tccaagtcttctgaaatccattccttgtaatctgcttataagttctaacaattttcagtttatcaaatataaatgtcttattgatattgccatctaa---cagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
|| | | | | | || ||| | ||||| | || | | | ||| || | | || || | || ||| | || ||||||||||| | ||||||||||| || ||||| ||||| |||||||| ||||| ||||| ||||||
tctgtgaataatcagaaacagcttctgttcattacttat---cccatgcatctcttactttcggaagtctctctgactagtgactactgctaaaaaattgcagATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAG
upper sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 10
tccaagtcttctgaaatccattccttgtaatctgcttataagttctaacaattttcagtttatcaaatataaatgtcttattgatattgccatctaacagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
| || || || || ||| | | || || || | || | | | || | | || | | ||||| ||||||||||||||||| || || || |||||||||||||| ||||||||||| || ||||||
---------------gtatgttgctggttgtcctcttctttactttattttttctctcctgctc---tcttgaaaggttgtctaatttctctccatgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAG
upper sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 10
tccaagtcttctgaaatccattccttgtaatctgcttataagttctaacaattttcagtttatcaaatataaatgtcttattgatattgccatctaacagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
| | | ||| | | ||||| | ||| | || ||| | ||| | | || || | || ||| | ||||| ||||||||||||||||| || || || |||||||||||||| ||||||||||| || || ||
-----------gtatgtgccgctcttcttttgtgcttctttactctctctcttccacagttagctaatct--ctttcctactaat-ttgt--ttctgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAA
upper sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 10
tccaagtcttctgaaatccattccttgtaatctgcttataagttcta-acaattttcagtt---tatcaaatataaatgtcttattgatattgcc-atct-aacagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
| || ||| || || || || | | | || | || |||| || | ||| | || |||| | || || | | | ||||||| ||||| || |||||||| |||||||||||||| ||||||||||| ||||| ||||| |||||
-----atattatgagatttatgccac-tatccaacatcctctttgtgcacttttttatattctgtgtcagaaccttatttcttccttatcttttctgtatgaacagATAGTAACCCTGGAAGATGTGGTTGAGGAAATTGTCGGTGAAATCTTCGATGAGAATGATTCAAAA
upper sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S147_55V6.1 (Physcomitrella patens), 3'ss of exon 12
-tccaagtcttctgaaatccattccttgtaatctgcttataagttctaacaa--ttttcagtttatcaaatataaatgtcttattgat-attgccatctaacagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
| ||| | || | | | | | || | | ||| || || |||| ||| | ||| | | | | |||| | | | |||| |||| || || ||||||||||| || || |||||||| ||||| |||||||||||||| || |||
ttgtaagggggattaattttaattca---actccaagttgaggttgtagtaaattttttgttttgtgcaatcaatacaaat-actgatgaacacagaattacagGTTGTGACACTGGAAGATGTTGTGGAAGAGATTGTTGGCGAAATTTTTGATGAAAATGATTCCAAG
upper sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S7_173V6.1 (Physcomitrella patens), 3'ss of exon 13
--tccaagtc--ttctgaaatccattccttgt-aatctgcttataagttctaacaattttcagtttatcaaatataaatgtcttattgatattgccatctaacagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
| ||| || | | |||| | | ||| | || | || ||| | | | | || || || | || | || | || ||||||| || ||||||||||| || || |||||||| || || || ||||||||||| ||||||
acttcaattcaactttaaaattaaggctgtgttgaatcatttgatatttgtaatcaatacaaataccgatgctaacaaagttgcacc-atgc-gttattt---agGTTGTAACGCTGGAAGATGTTGTGGAAGAGATTGTTGGGGAGATTTTCGATGAAAATGATTCAAAG
upper sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S58_81V6.1 (Physcomitrella patens), 3'ss of exon 13
-----------------------------------------------------------tccaagtcttctgaaatccattcc--ttgtaatct----gcttataagt----tctaacaattttcagtttat---caaatataaatgtctt--attgatattgc-catctaacagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
||| | | | || ||| | ||||| |||||||| | | | | ||| || || |||| |||| | ||| | | | | ||| |||| || | ||||| |||||||| ||||||||||||||||| |||||||||||||| || |||
gtaagatttgaaaagcacatgacaactaatctgatagaatatttatagtctctgttgtgagcaatttcaagggagtctatttcaactgtaagaatagggcttataattagccccctgctttcctcacttgatatttgaatactaatggaatcaatttacgtgatacgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGATGAAAATGATTCGAAG
upper sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ38618 (Selaginella moellendorffii), 3'ss of exon 10
tccaagtcttctgaaatccattccttgtaatctgcttataagttctaacaattttcagtttatcaaatataaatgtcttattgatattgccatctaacagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
|| ||| | || |||| | | || | || | | | | || ||||||||||| || ||||||||||||||||| |||||||| ||||| ||||| ||||| || || |||
-------------------------------------gtacgtttcatatcttcgtagttctt----ttcgggagtataat--acacttctatt--gcagATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAG
upper sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ31527 (Selaginella moellendorffii), 3'ss of exon 10
tccaagtcttctgaaatccattccttgtaatctgcttataagttctaacaattttcagtttatcaaatataaatgtcttattgatattgccatctaacagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
|| || |||| | | || | || | | | | || ||||||||||| || ||||||||||||||||| |||||||| ||||| ||||| ||||| || || |||
---------------------------------------------gtacgtttcatagttctt----ttcgggagtataat--acacttctatt--gcagATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taacaattttcagtttatcaaatataaatgtcttattgatattgccatctaacagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
tttatcaaatataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccaagtcttctgaaatccattccttgtaatctgcttataagttctaacaattttcagtttatcaaatataaatgtcttattgatattgccatctaacagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
- - - tcttctg
- - - - - - - - -ccattcc
- - - - - - - - - - - - - - - tctgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatataa