Sequence
atgc intronic sequence ATGC exonic sequence...tgcccctttaattagtaaaataatcttaattttgtttttaatccaagccatatatttgtgatagtaataactttgttttttattttttttggtgtgacagGGAACTTGCAAAAGATTTTGCAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG
Basic information
species | Glycine max |
transcript | GLYMA06G11930.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11930.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g08520.1 (Oryza sativa), 3'ss of exon 4
----tgcccctttaattagtaaaataatcttaattttgtttttaatccaagccatatatttgtgatagtaataactttgttttttattttttttggtgtgacagGGAACTTGCAAAAGATTTTGCAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG
|| | | || | | | || || ||| || | ||||||| | | | ||| | | | || | || | ||||||||| || |||||||||| || |||||||||| || || || || ||||||||||||||||| |||| |||||| ||||
ttgatgatacctatcttttcactttgtaccatatgctgatttactgccttgttttatatttttaaggttcata---ctaatcaaaggtgattcttgtaag-cagGGAACTAGCGAAAGATTTTGTGGTTTCTGGCACTGCTTCAGAATCACTATATGGTGCTTGTGAGTCCATGTATAAGCCAAGCATG
upper sequence: GLYMA06G11930.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g43570.1 (Oryza sativa), 3'ss of exon 5
-tgcccctttaattagtaaaataatcttaattttgtttttaatccaagccatatatttgtgatagtaataactttgttttttattttttttggtgtgacagGGAACTTGCAAAAGATTTTGCAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG
| | | | || | | | | || | | | | | || | | | | || || ||| || |||| ||||||||| || || ||||| | || | || || ||||| |||||||| ||||||||||||||||| |||| || || |||||
ttttggtctaagtccgtgtgcctgatatgtctgattaggcgtttgaacgcttgtttctcatattcttgtgagctgattgaggatgtttatttctgtg-cagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATATGGTGCTTGTGAGTCCATGTACAAACCAAACATG
upper sequence: GLYMA06G11930.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G117544_T02 (Zea mays), 3'ss of exon 3
tgcccctttaattagtaaaataatcttaattttgtttttaatccaa---gccatatatttgtgatag-taataactttgttttt-tattttttttggtgtgacagGGAACTTGCAAAAGATTTTGCAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG
| | | | |||| || | || | || | | ||||||| || | ||| || | ||||| ||| | ||||||||| ||||||||||||| || | || ||||| || ||||| |||||||||||||||||||| |||| |||||| |||||
taatgttaagcctgttgaaat--tcgttccttacatcctatactgacttgccatatggcctctctaccttgtaatcttatcagagtatttccttttatt---cagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATG
upper sequence: GLYMA06G11930.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g02260.t01 (Vitis vinifera), 3'ss of exon 4
tgcccctttaattagtaaaataatcttaattttgtttttaatccaagcc-atatatttgtgatagtaataactttgttt--tttattttttttggtgtgac-agGGAACTTGCAAAAGATTTTGCAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG
| | |||| || | ||| | ||| ||||| | | || | ||| | ||| ||| ||| ||| | || || | ||||| ||||| |||||||||| || ||||| ||||| || ||||||||||||||||| || ||| | ||||| ||||| ||||||
---ttgtctgatta-taggttgatccaagctttctttttgggtgatattgacattatggtgctttacctaattttctttaatttttcttcttcctcacatccagGGAGCTTGCTAAAGATTTTGTTGTTGCTGGTACTGCCTCTGAGTCTCTTTATGGTGCCTGCGAGGCCATGTTCAAGCCCGACATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agccatatatttgtgatagtaataactttgttttttattttttttggtgtgacagGGAACTTGCAAAAGATTTTGCAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG
taataac putative branch site (score: 1)
ctttgttttttatttt CT-rich tract
tatatttgtgatagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcccctttaattagtaaaataatcttaattttgtttttaatccaagccatatatttgtgatagtaataactttgttttttattttttttggtgtgacagGGAACTTGCAAAAGATTTTGCAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG
- ccccttt
- - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - ccaagcc