Sequence
atgc intronic sequence ATGC exonic sequence...agaggcttgtactggtgtactctgtttgaatgtgttctagacattgactatattatatatttcagatttcttattgtgatttgtattgttgttcttaaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAG
Basic information
species | Glycine max |
transcript | GLYMA08G21830.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 5
agaggcttgtactggtgtactctgtttgaatgtgttctagacattgactatattatat--atttcagatttcttattgtgatttgtattgttgttctt--aaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAG
| | | |||| | | | | | | | | |||||| || | || | || | || || | | || | |||||||||| || ||||| || |||||||| ||||| | ||| ||||| || ||||||||| |||| || ||||| |||||||||||||| ||||||| |
----tacagcattagtgtgttatatacaggctctctgtttatgattctcaagttatatggatgttagttaaagagctgaaacttcagttatcaattttgtacagGATGTTACGCTTCATGACCTTGATGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGACAGATGATGAAGCCACGGAAAACTG
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 5
--agaggcttgtactggtgtactctgtttgaatgtgttctagacattgactatattatatatttcagatttcttattgtgatttgtattgttgttcttaaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAG
| | || || | ||| | || | | || | | | ||||| | | || | | | | | || | || |||||||||| || ||||| || || ||||| ||||| | ||| ||||| || ||||||||| |||| || ||||| || ||||||||||| | || || |
tcatatgca-gtgttagtgcattcaatctttctgcttatggctcttaagttatatggaagttaatgaatataggaaaacttctcctgtcatt-tatgtacagGATGTTACACTTCATGACCTTGACGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTG
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------agaggcttgta--ctggtgtactct-gtttgaatgtgttctagacattgactata---ttat--atatttcagatttcttattgtgatt-tgtattgttgttcttaaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAG
| || | ||| | | | ||||| |||||| || | | | || |||| | | | | || || | || | || | ||| || | ||||||| || || || ||||||||||| || ||||| ||||||||||| || || ||||| || ||| ||||||| || |||||||| || |||| || |
gtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttga-ctgatagGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTG
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
--agaggcttgtactggtgtactctgtttgaatgtgttctagacattgactatattatatatttcagatttcttattgtgatttgtattgttgttcttaaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAG
| || | | | | || || | | || | || ||| |||| |||| |||| ||| || | | ||||||| || || ||||| ||||||||||| |||||||| |||||||| ||||||||||| |||| || |||||||||||||||||||||||||||||||
ctaaagttacatctttataaggtgtggtttcagagacacagtgggttccccatgttaattattc--atcttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------agaggcttgtactggtgtactctgtttgaatgtgttctagacattgactatattatatatttcagatttcttattgtgatttgtat-tgttgttct-taaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAG
| ||| || ||||| | |||| | | | || | ||| | ||| | |||||| |||| ||| |||| | | | ||||||| || || |||||||| |||||||| ||||| || |||||||| || |||||||| |||| ||||||| ||||||||||| || | || || |
gttagtgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatattttatgcttgtaatcttatgcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 5
agaggcttgtactggtgtactctgtttgaatgtgttctagacattgactatattatatatttcagatttcttattgtgatttgtattgttgttcttaaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAG
| | ||| | | || ||||| | | || | |||| || || || |||||||| |||||||| ||||| || |||||||| |||||||||||||| || ||||||| |||||||||||||| | || || |
----------------------------------------gtactaactgtgaagaaagggtccagtttctcttcacacagcaagtgtgggtgtatgtagGACGTCACACTGCATGATCTAGATGCTGCAAATGCGCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTG
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ33466 (Selaginella moellendorffii), 3'ss of exon 5
agaggcttgtactggtgtactctgtttgaatgtgttctagacattgactatattatatatttcagatttcttattgtgatttgtattgttgttcttaaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAG
| | ||| | | | || ||||| | | | ||| | |||| || || || |||||||| |||||||| ||||| || |||||||| |||||||||||||| || ||||||| |||||||||||||| | || || |
----------------------------------------gtactaactgtgatgaaagggtccagtttctcttcacacagcaagtgggtgtattc--agGACGTCACACTGCATGATCTAGATGCTGCAAATGCGCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|151406331|gb|EV276146.1|EV276146EST: ATGTTCCACTGCCTAAGGGAGAGGTTCACNNNNNNNNGGAGATTGTTCAG GATGCTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGA
genomic: ATGTTCCACTGCCTAAGGGAGAGGTTCACAAAAAAAAGGAGATTGTTCAGgtatttaatt ... gttcttaaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gactatattatatatttcagatttcttattgtgatttgtattgttgttcttaaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAG
cattgac putative branch site (score: 3)
ttgttctt putative PPT
tattatatatttcaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaggcttgtactggtgtactctgtttgaatgtgttctagacattgactatattatatatttcagatttcttattgtgatttgtattgttgttcttaaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - actggtg
- - - - - - - - - - -ctgtttg
- - - - - - - - - - - - - - - tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg