Sequence
atgc intronic sequence ATGC exonic sequence...acggcaataagatgtcagcatattaatttcatatataatgtttcaaaaataaaattcttagaaattcaaattgaatacaggtaaatcaccttgaatgcagGAGATGGACTACAATAATGAAGCAAGCAATGGTATCAAGTTCAG
Basic information
species | Glycine max |
transcript | GLYMA16G27500.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G27500.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g54790.1 (Oryza sativa), 3'ss of exon 6
acggcaataagatgtcagcata-ttaatttcatatataatgtttcaaaaataaa------attcttagaaattcaaattgaatacaggtaaatcaccttgaatgcagGAGATGGACTACAATAATGAAGCAAGCAATGGTATCAAGTTCAG
|| |||| | || || || || | || || |||||||| ||||||||| | || |||||||||||||||||||| || ||||||||||||||| |||| |||||||| | ||| | || |||||
-----tattctatgtacacttagctagttagctacctgat--tttaaaaataaggttcatattcttagagctacacattgaatacaggtaaatcacatttaatgcagGAGATGGATTACAGAGCAGAAGCAAGAAGTGGGCTTAAATTCAG
upper sequence: GLYMA16G27500.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G305007_T02 (Zea mays), 3'ss of exon 5
acggcaataagatgtcagcatatta-atttcatatataatgtttcaaaaataaaattcttagaaattcaaattgaatacaggtaaatcaccttgaatgcagGAGATGGACTACAATAATGAAGCAAGCAATGGTATCAAGTTCAG
| | | || || |||| | | | ||| | | || | | |||||| ||||| |||||||||||||||||||| || |||||||||||||| || | | |||||||| ||||| | ||||||||
gtgctagcagtattctaggctattgcagattctgactaaaacattaggtgtata-tccttagatattcacattgaatacaggtaaatcacatttgatgcagGAGATGGATTATAGAGAAGAAGCAAGAAATGGACTTAAGTTCAG
upper sequence: GLYMA16G27500.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G71810.1 (Arabidopsis thaliana), 3'ss of exon 6
acggcaataagatgtcagcatattaatt-tcatatataatgtttcaaaaataaaattcttagaaattcaaattgaatacaggtaaatcaccttgaatgcagGAGATGGACTACAATAATGAAGCAAGCAATGGTATCAAGTTCAG
| || | | | | || || | || |||| | | || ||||||| || | ||||||||||||||||||| |||||||||||||||||| ||| |||||||| || || || || || ||
-ttgaaagattgtttagatggactagttgttgcatttaattcgtgttcgaggaatatcttagagctttatattgaatacaggtaaatcaaattgaatgcagGAGATGGATTACTTGAATGAAGCTCAAAACGGAATAAAATTTAG
upper sequence: GLYMA16G27500.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0001g01620.t01 (Vitis vinifera), 3'ss of exon 6
-acggcaataagatgtcagcatattaatttcatatataatgtttcaaaaataaaattcttagaaattcaaattgaatacaggtaaatcaccttgaatgcagGAGATGGACTACAATAATGAAGCAAGCAATGGTATCAAGTTCAG
| ||| | || | || || | | ||| | || | | | ||||||| |||| |||||||||||||||||||| ||||||||||||||||||||| | || ||||| | ||||| |||||||| ||
aagcattttaaaacttcttttttttttttccttttatcct-ttgctctaggcattttcttagtgcttcatattgaatacaggtaaatcacattgaatgcagGAGATGGACTATAGAAAAGAAGCGAAGAATGGGATCAAGTTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaataaaattcttagaaattcaaattgaatacaggtaaatcaccttgaatgcagGAGATGGACTACAATAATGAAGCAAGCAATGGTATCAAGTTCAG
tcacctt CT-rich tract
aaaattcttagaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acggcaataagatgtcagcatattaatttcatatataatgtttcaaaaataaaattcttagaaattcaaattgaatacaggtaaatcaccttgaatgcagGAGATGGACTACAATAATGAAGCAAGCAATGGTATCAAGTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcacc