Sequence
atgc intronic sequence ATGC exonic sequence...atgatgatagttttgctaagttttctgttgatttgcatgtttaggtgatcatattatgatgccaagaatcctaatcattatatggtgtcatgatctgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
Basic information
species | Glycine max |
transcript | GLYMA04G31180.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g49570.1 (Oryza sativa), 3'ss of exon 8
atgatgatagttttgctaagttttctgttgatttgcatgtttaggtgatcatattatgatgccaagaatcctaat-cattatatggtgtcatgatctgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
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----------------------gtaagttatgcttcagatttcaccaatt-tattagca-gcagagtttcgttatgtattggttgttgttatttgaactagGATGTGGCGGGAAATTCGACTCCTAGCTGACACCAAGCCTGTGGTTGCTTCAATGTCTGATGTTGCTGCAAGTGGTGGGTACTACATGGCAATGGCTGCA
upper sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G122843_T02 (Zea mays), 3'ss of exon 13
atgatgatagttttgctaagttttctgttgatttgcatgttta-ggtgatcatattatgatgccaagaatcctaatcattatatggtgtcatgatctgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
| |||| || | | |||||||| | | | | | | | | | |||| | | || |||||||||||||||||||| ||| | || || ||||| || ||||||| ||||||||||| || |||||||| || |||||||||||||||| ||
-----gtaagttacgccttaggatttagtgatttgcttctcagcagcagcagcagcagagttttttcagtaaca--tattacgaattcttatttcaactagGATGTGGAGAGAAATCCGACTTCTAGCCAACTCTAAACCTGTAGTTGCTTCGATGTCTGATGTTGCTGCAAGTGGGGGCTACTACATGGCAATGGCTGCA
upper sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 8
-atgatgatagttttgctaagttttctgttgatttgcatgtt-taggtgatcatattatgatgccaagaatcctaatcattatatggtgtcatgatctgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
|| ||| | | | || | ||| |||||| || | ||| | | || | | || ||||| | || | ||| | | ||| |||||||| || ||| || |||||| ||||||| |||||||| |||||||| |||||||||||||||||||| |||||||||||||||| ||
tatctatctagcctag--aggtcatgtgtggatttgaatttaatagctttggaaatccttctaggctttattataatcttcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA
upper sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv17s0000g04690.t01 (Vitis vinifera), 3'ss of exon 4
----atgatgat-agttttgctaagttttctgttgatttgcatgtttaggtgatcatattatgatgccaagaatcctaatcattatatggtgtcatgatctgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
| ||| | | ||| | | | ||| | | | ||| | | | ||| ||| | || ||| | | | || || |||| |||||||| |||||| | ||| ||||||| |||||||| |||||||| ||||||||||||||||| || || ||||||||||||||||||||||||||
gcttgtacagatgaaaaaagagaaggaatgagaaaagaaaaatgcat-gacaaatataatgagctcccactaat--tggtccttaatttttatgattat--gcagAATGTGGAGGGAAATCAGACTTCTGGCTGCCTCAAAACCTGTCATTGCATCAATGTCTGATGTGGCTGCTAGCGGAGGGTACTACATGGCAATGGGAGCA
upper sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S25_21V6.1 (Physcomitrella patens), 3'ss of exon 11
-atgatgatagttttgctaagttttctgttgatt-tgcat-gtttaggtgatcatattatgatgccaagaatcctaatcattatatggtgtcatgatctgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
| | | | | ||| | | ||||| ||||| ||| || | | | || | | | || || ||| | | ||| | | | ||||||||| | |||||| || | |||| ||| ||||| ||||| |||||| | || || ||||| |||||||| |||||||||||||||| |||
cgtaaaaaagctgcttataactgtattgttgtcagtgcatcaattacgttaccgttttcctacttctgaa---cttataatttttcgttgttacggccattagGATGTGGCGGGAAATCAAACTCCTAGCTGAAAGAAAGCCAGTGATTGCATCAATGGCCGACGTAGCAGCTAGTGGAGGCTACTACATGGCAATGGCAGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatcatattatgatgccaagaatcctaatcattatatggtgtcatgatctgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
tcctaat putative branch site (score: 2)
taatcattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgatgatagttttgctaagttttctgttgatttgcatgtttaggtgatcatattatgatgccaagaatcctaatcattatatggtgtcatgatctgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
-tgatgat
- - - - - - -tgctaag
- - - - - - - - - - - -tctgttg
- - - - - - - - - - - - - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgtc