Sequence
atgc intronic sequence ATGC exonic sequence...attgggattgttggtccttgaaaacaatcatggtcttttttactataactcctataagtctgatctagtttcttttttgtatgttgtgttgtctatatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGAACAACAGCGGAGCCAGGCTCTTGAAGCACATGCTGCATCATTTGCTCAATTCAAA
Basic information
species | Glycine max |
transcript | GLYMA11G35460.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 5
attgggattgttggtccttgaa-aacaatcatggtcttttttactataactcctataagtctgatctagtttcttttttgtatgttgtgttgtctatatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGAACAACAGCGGAGCCAGGCTCTTGAAGCACATGCTGCATCATTTGCTCAATTCAAA
|| | | || || | | | || || || || | | | ||| | | || | | | | || ||||||||||| |||| || ||||| |||||||| || |||||||| || || || || ||||| |||||||| ||||| ||||| ||||| ||| ||
atatgctacacctatgctggagcagttcttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcacccat-cagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 5
attgggattgttggtccttgaaaacaatcatggtcttttttac-tataactcctataagtctgatctagtttcttttttgtatgttgtgttgtctatatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGAACAACAGCGGAGCCAGGCTCTTGAAGCACATGCTGCATCATTTGCTCAATTCAAA
|| | | || ||| | | ||| |||| || || | | | ||| | | || | | | | || ||||||||||| |||| || ||||| |||||||| || |||||||| || || || || ||||| |||||||| ||||| ||||| ||||| ||| ||
atatgctacacctatgctggaacagtttttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcacccat-cagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
attgggattgttggtccttgaaaacaatcatggtctttt-ttactataactcctataagtctgatc--tagtttcttttttgtatgttgtgttgtctatatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGAACAACAGCGGAGCCAGGCTCTTGAAGCACATGCTGCATCATTTGCTCAATTCAAA
| | || || || | ||| | | | || || ||| | | | || | | || | | | | | ||||| | ||||||||| |||||||| ||||| || ||||||||||| ||||||||||| ||||| ||||| |||||||||||||| ||||| || || ||
-gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatcttgtcattattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
attgggattgttggtccttgaaaacaatcatggtcttttttactataactcctataagtctgatctagtttcttttttgtatgttgt-gttgt----ctatatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGAACAACAGCGGAGCCAGGCTCTTGAAGCACATGCTGCATCATTTGCTCAATTCAAA
| || || || || | | | || | | ||||| | | | || | || || || | || |||| || | || | ||||| ||||||||||| |||||||| ||||| || ||||||||||| ||||||||||||||||| |||||||||||||||||||| |||||||| || ||
-gtagggttcctgcaccacgtattaggt--tgaattaagacatcataacggcagtca---tgttgtatatttttgacggaatcttgtcattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 5
--attgggattgttggtccttga-aaacaatcatggtc--ttttttactataactcctataagtctgatctagtttcttttttgtatgttgtgttgtctatatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGAACAACAGCGGAGCCAGGCTCTTGAAGCACATGCTGCATCATTTGCTCAATTCAAA
||| | ||||| ||| ||| | | || |||||| | | |||| |||||| ||| ||| || | | || | || |||||||||| | || ||||| || ||||| || |||||||| ||||| || || || || ||||||||||| |||||||||||||| || || |||
ttgttgttttacttggttgttgggaaatctttctcctcagttttttcagagatttcctggtgttctgat----tttaatttccacatcctat-ttatgcttacagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 3'ss of exon 5
-attgggattgttggtccttgaaaacaatcatggtcttttttactataactcctataagtctgatctagtttcttttttgtatgttgtgttgtctatatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGAACAACAGCGGAGCCAGGCTCTTGAAGCACATGCTGCATCATTTGCTCAATTCAAA
| | | | ||| | || || ||| | | | | | | | | | | | || || | | || |||| ||| | || |||||||||||||| | || || ||||| || ||| |||| ||||| |||||||| |||||||| ||||||||| | |
atctctcctcagcaacctcttgaaattttaattatcgtttagagttggttcctttctcatttaacactgcattgacagttcttatttctctggtt-ttcagCGGCCCCAACTTGTGAAAGGAAACATGCAGTTGTTTTCAGTGGACCAGCAGAGGAGTCAGGCGCTTGAAGCTCATGCTGCGTCATTTGCTTCCCACCAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 5
attgggattgttggtccttgaaaacaatcatggtcttttttactataactcctataagtctgatctagtttcttttttgtatgttgtgttgtctatatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGAACAACAGCGGAGCCAGGCTCTTGAAGCACATGCTGCATCATTTGCTCAATTCAAA
| | ||| |||||||| | || | | ||| | |||||| |||| |||||||||||||||||||| || || || || ||||| || || ||| | ||||| ||||||||||| || ||| ||||||
-------------------------------------------------gtatccatttcttgaaaagtttcttgtagcta-acaaagaaactcttttagCGTCCACAACTGGTGAAAGGAAACATGCAACTCTTTTCAGTCGATCAGCAGCGAAGTCAAGCTTTGGAAGCTCATGCTGCATCTTTCGCTACATTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taactcctataagtctgatctagtttcttttttgtatgttgtgttgtctatatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGAACAACAGCGGAGCCAGGCTCTTGAAGCACATGCTGCATCATTTGCTCAATTCAAA
tttcttttttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgggattgttggtccttgaaaacaatcatggtcttttttactataactcctataagtctgatctagtttcttttttgtatgttgtgttgtctatatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGAACAACAGCGGAGCCAGGCTCTTGAAGCACATGCTGCATCATTTGCTCAATTCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- -gggattg
- - - - - - -gtccttg
- - - - - - - - - - aaaacaa
- - - - - - - - - - - - - - catggtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtg