Sequence
atgc intronic sequence ATGC exonic sequencegtatggctagatttctgcaagtattctctgtcagggtttttaggattgtcaggttatgttgacaaatttttcattctagGTGATAATTTGGTGGGCTGGTCTTATGAGAGGTGCTGTTTCAATGGCACTTGCCTACAATCAG
Basic information
species | Glycine max |
transcript | GLYMA19G42900.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 10
------gtatggctagatttctgcaagtattctctgtcagggttttta---ggattgtcaggttatgttgacaaatttttcattctagGTGATAATTTGGTGGGCTGGTCTTATGAGAGGTGCTGTTTCAATGGCACTTGCCTACAATCAG
|| | | | | | || || || || ||| | |||||||| || | | | |||| |||| || ||||||||||| ||||| |||||||||||||| || || ||| | |||||||| ||
gtgagtgttttatttagcagcatcttaggcttgctatcttctcttataaggggactttcaggttac-ttatgatgtgggttattc-agGTTATTATTTGGTGGGCGGGTCTGATGAGAGGTGCTGTGTCCATTGCATTGGCCTACAACAAG
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 12
-------------------------gtatggctagatttctgcaagtattctctgtcagggtttttagga--ttgtcaggttatgttgacaaatttttcattctagGTGATAATTTGGTGGGCTGGTCTTATGAGAGGTGCTGTTTCAATGGCACTTGCCTACAATCAG
| | | | || || ||| || ||| | ||| | | ||| ||| | ||||||| || || |||||||| ||||| |||||||| || || ||||| ||||||||||| | ||
gttagtattgaccttttttattcttatgtagttgtatcacttt---ctttccctcctgaaaacagagggagctaagcagctaactgtgatgggtttatt-ctctagGTAATCATATGGTGGGCAGGTCTCATGAGAGGAGCAGTATCAATAGCACTTGCCTATCACAAG
upper sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 11
-------------gtatggctagatttctgcaagtattctctgtcagg-gtttttaggattgtcaggttatgttgacaaatttttcattctagGTGATAATTTGGTGGGCTGGTCTTATGAGAGGTGCTGTTTCAATGGCACTTGCCTACAATCAG
| | || ||| | || | | || | | | | | ||| || | | | ||| ||| | ||||| ||||| |||||||||||||| ||||| |||||||| || |||| ||||| || ||||||
gtgggtgcttccttttttccttgatgtttggagttcatcattctaacttaccaattgaattaccaaatcttatcaacatttttcattgtgtagGTTATAATATGGTGGGCTGGTCTCATGAGGGGTGCTGTGTCTGTGGCCCTTGCTTATAATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctgtcagggtttttaggattgtcaggttatgttgacaaatttttcattctagGTGATAATTTGGTGGGCTGGTCTTATGAGAGGTGCTGTTTCAATGGCACTTGCCTACAATCAG
tgttgac putative branch site (score: 3)
tttttcattct putative PPT
aaatttttcattcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggctagatttctgcaagtattctctgtcagggtttttaggattgtcaggttatgttgacaaatttttcattctagGTGATAATTTGGTGGGCTGGTCTTATGAGAGGTGCTGTTTCAATGGCACTTGCCTACAATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT