Sequence
atgc intronic sequence ATGC exonic sequence...tattgaatttttttacctttagttggttttgcatttttgctcaatgatgtgagcaattggattttacatggaactaatggagtttgcctcctctctatagACTCAAGGGCGTGAATCAATTGCGGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTTGCTTGTGACCTTCATTCAGGGCAGT
Basic information
species | Glycine max |
transcript | GLYMA17G16400.4 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G16400.3 (Glycine max), 3'ss of exon 3
lower sequence: AT2G35390.3 (Arabidopsis thaliana), 3'ss of exon 2
------------tattgaatttttttacctttagttggttttgcatttttgctcaatgatgtgagcaattgg--attttacatggaactaatggagtttgcctcctctctatagACTCAAGGGCGTGAATCAATTGCGGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTTGCTTGTGACCTTCATTCAGGGCAGT
| | ||| ||| || | || | | | |||| | || | | ||| ||||| || || |||| ||| | | | | || | |||| |||||||||||||| ||||| || ||| | ||||| || ||||| || ||||||| ||||| || |||||||||||||| ||||||||||| ||||
gtaaagtctctttgtgtggtttagctactttcacatgatatggagggtttg-ttgataactt-agctattggtaatcttttctggataaaattgtatgt-tttgctgcttgcagACACAAGGGCGTGAATCCATTGCTGCCAAATTGGTTGCAAATCTTATCACTGAAGCTGGTGCAGATCGAGTTCTTGCTTGTGATCTTCATTCAGGACAGT
upper sequence: GLYMA17G16400.3 (Glycine max), 3'ss of exon 3
lower sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 3
tattgaatttttttacctttagttggttttgcat-ttttgctcaatgatgtgagcaat-tggattttacatggaactaatggagtttgcctcctctctatagACTCAAGGGCGTGAATCAATTGCGGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTTGCTTGTGACCTTCATTCAGGGCAGT
|| |||| | | | || |||||| | || | || || | | || ||| | | | | | | |||| |||||||||||||| ||||| || ||| | || || |||||||| ||| |||| || ||||| | ||||| |||||||| ||||||||||| || |
---------------------gtaggttctttttgtcttcttcaatggtagatacagtatgtcaagtaatttcatctgatgtatcta--ttgatgttttcagACACAAGGGCGTGAATCTATTGCTGCCAAATTGGTAGCAAACCTTATAACAGAAGCCGGTGCAGATAGGGTTCTGGCTTGTGATCTTCATTCAGGACAAT
upper sequence: GLYMA17G16400.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 3
tattgaatttttttacctttagttggttttgcatttttgctcaat--gatgtgagcaattggattttacatggaactaatggagtttgc-ctcctctctatagACTCAAGGGCGTGAATCAATTGCGGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTTGCTTGTGACCTTCATTCAGGGCAGT
| ||| | | || | | | | | || || ||| |||| || |||| | || || | | || | ||||| ||||||||||||||||||| ||||| |||||||||||||| || |||| || ||||| || || |||||||||||||||||||| |||||||| |||||||
-actgagaaatgatgggttgaacaa--tctacgtcatttctaaattggatgctagaaatttacatgtaaattacatcttcttcatctgtatttttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgtgagcaattggattttacatggaactaatggagtttgcctcctctctatagACTCAAGGGCGTGAATCAATTGCGGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTTGCTTGTGACCTTCATTCAGGGCAGT
aactaat putative branch site (score: 2)
tttgcctcctctctat putative PPT
attttacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattgaatttttttacctttagttggttttgcatttttgctcaatgatgtgagcaattggattttacatggaactaatggagtttgcctcctctctatagACTCAAGGGCGTGAATCAATTGCGGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTTGCTTGTGACCTTCATTCAGGGCAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - -gttggtt
- - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - tgatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaatgg