Sequence
atgc intronic sequence ATGC exonic sequence...tgctataaatatttagatatacgttttttgtttttcattctcactcctgagttttattatactgaaaaggtctcctgtagttatgagtttccttttctagGTTGCTCGTGGTGACAAGGCCGGTGGTGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTG
Basic information
species | Glycine max |
transcript | GLYMA20G39260.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G39260.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os11g24540.2 (Oryza sativa), 3'ss of exon 10
-tgctataaatatttagatatacgttttttgtttttcattctcactcctgagttttattatac-tgaaaaggtctcctgtagttatgagtttccttttctagGTTGCTCGTGGTGACAAGGCCGGTGGTGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTG---
|| ||| ||| | | || | | | | | || | || | | |||| | | | | || | | || | | || | |||||||||||||||| || | ||| ||||||||||| ||||| || ||| | |||||| | | |||||| |||||||||||||| ||||| || ||||
ttgatatgtgtatcttcagttagatctgtcctgtaagatatac-cttttatctattatgaagtgttatagtgttagatatgattctatccatactgcac-agGTTGCTCGTGGTGATAACTC---TGGGGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG
upper sequence: GLYMA20G39260.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G05820.1 (Arabidopsis thaliana), 3'ss of exon 10
--tgctataaatatttagatatacgttttttgtttttc-attctcactcctgagttttattatactgaaaaggtctcctgtagttatgagtttccttttctagGTTGCTCGTGGTGACAAGGCCGGTGGTGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTG
| | ||| || | | | || | | |||| || ||| || | | | | ||| |||| | | | ||| | |||||||| ||||| ||| | | ||| ||| | ||||| |||||||||||| |||| || ||||||||||| |||||||| || | ||||| || ||||
cacatagcgagaacgaagaaggtcgatgataggttaactaacctcaatcac--gttctagttgattactatattcttctgtttgtgtaaattta-tggcatagGTTGCACGTGGGAGCAAAGACACTGGAGAATCTATTCCCATGCTTTTGAGAATTCCACGGCTTTCTGATCCATGGGGTGGTTACAACATGATCGGTTTTG
upper sequence: GLYMA20G39260.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 10
tgctataaatatttagatatacgttttttgtttttcattctcactcctgagttttattatactgaaaaggtctcctgtagttatgagtttccttttct------agGTTGCTCGTGGTGACAAGGCCGGTGGTGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTG
| |||| || | || | | || | | || || | | | || || | | | | | | | ||| | | | | ||||| | ||||||||||||||||||| ||||| ||| | ||||| ||||| |||||| |||||||| | | ||||||||||||||| |||||||||||||| ||||
ttctattaacacctataaa------ttcagaatgacaacctaaatatttagattcaccacaattagacaaatttctggtatgagttctcttcttttgtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgagttttattatactgaaaaggtctcctgtagttatgagtttccttttctagGTTGCTCGTGGTGACAAGGCCGGTGGTGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTG
tttccttttct CT-rich tract
ttttattatactgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgctataaatatttagatatacgttttttgtttttcattctcactcctgagttttattatactgaaaaggtctcctgtagttatgagtttccttttctagGTTGCTCGTGGTGACAAGGCCGGTGGTGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTG
tgctata
- - - - - - - - - - - - - - - - -ttcattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctgt