Sequence
atgc intronic sequence ATGC exonic sequencegtcactataagtttttttaagttttcctttcaactgtttttgtggctgcaagtatatgtgtgtttttgctacgtgtactaattccatatggtaatttaaaaccagGGAACTATAGCACATGCTTTAGAGAAGACCAAGTATGAAGACTCAGATGTCAAGTGGAAAGAGTTGGACCCCAAGTACCACTTCTCGTGTCAATTCATGG
Basic information
species | Glycine max |
transcript | GLYMA14G39070.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G39070.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G060659_T01 (Zea mays), 3'ss of exon 8
gtcactataagtttttttaagttttcctttcaactgtttttgtggctgcaagtatatgtgtgtttttgctacgtgtactaattccatatggtaat-ttaaaaccagGGAACTATAGCACATGCTTTAGAGAAGACCAAGTATGAAGACTCAGATGTCAAGTGGAAAGAGTTGGACCCCAAGTACCACTTCTCGTGTCAATTCATGG
| | | || | | || || ||| | | ||||| | | ||| | || | | | || ||| ||||| || || || || ||| |||||||||| ||||||||||| |||||||| ||||||| ||| |||| | |||||||| ||||| || ||||||| |
----------------gtgaagtgatgggccatcaagtagagtc-ttgaaagattgattactttttttttgctagtatga--cacagaagatgatcttattgacagGGGACAATCGCGCACGCTCTAGAGAAGACAAAGTATGAAGATTCAGATGTGAAGTGGAGAGATCTGGATCAGAAGTACCATTTCTCCTGCCAATTCACTG
upper sequence: GLYMA14G39070.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G37180.1 (Arabidopsis thaliana), 3'ss of exon 7
gtcactataagtttttttaagttttcctttcaactgtttttgtggctgcaagtatatgtgtgtttttgct-acgtgtactaattcca-tatggtaatttaaaaccagGGAACTATAGCACATGCTTTAGAGAAGACCAAGTATGAAGACTCAGATGTCAAGTGGAAAGAGTTGGACCCCAAGTACCACTTCTCGTGTCAATTCATGG
|| |||| |||| || | ||| | || | || | || || | | | ||| | | || ||| | ||| |||||| |||||||| || |||||||| || |||||||| |||||| |||||||||||||||| || || || || || ||||| | |||||| | ||
-----------gttctttacctttttactttgg-taaatttagaccaataaat-tactcattcttatgtcgaaacaaatttattgaaatgaaagaaaaaaaatctagGCAACTATTGCACATGCCTTGGAGAAGACTAAATATGAAGATTCAGATATCAAGTGGAAAGAGTTTGATCCTAAATATCATTTCTCATCTCAATTTACGG
upper sequence: GLYMA14G39070.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv04s0079g00230.t01 (Vitis vinifera), 3'ss of exon 8
gtcactataagtttttttaagttttcctttcaactgtttttgtggctgcaagtatatgtgtgtttttgctacgtg--tactaattccatatggtaatttaaaaccagGGAACTATAGCACATGCTTTAGAGAAGACCAAGTATGAAGACTCAGATGTCAAGTGGAAAGAGTTGGACCCCAAGTACCACTTCTCGTGTCAATTCATGG
|| |||||| || | | | ||| | || | || | ||| || |||||| | ||||||| || | | |||| |||||||||| |||||||| ||||||||||| ||||| ||||| || |||||||| ||||| || || || ||||| || || ||||| || ||||| | |
----------gtgtttttactcattagtggtagatagttt-gctactaaatataaac-tgtcttcttgctagctacttactaatc---taaaatgccctgaaactagGGAACTATTGCACATGCCTTAGAGAAGACTAAGTACGAAGATTCGGATGTCAAATGGAAGGAATTAGAGCCCAAATATCATTTCTCATGCCAATTTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtatatgtgtgtttttgctacgtgtactaattccatatggtaatttaaaaccagGGAACTATAGCACATGCTTTAGAGAAGACCAAGTATGAAGACTCAGATGTCAAGTGGAAAGAGTTGGACCCCAAGTACCACTTCTCGTGTCAATTCATGG
tactaat putative branch site (score: 1)
atatggtaatttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcactataagtttttttaagttttcctttcaactgtttttgtggctgcaagtatatgtgtgtttttgctacgtgtactaattccatatggtaatttaaaaccagGGAACTATAGCACATGCTTTAGAGAAGACCAAGTATGAAGACTCAGATGTCAAGTGGAAAGAGTTGGACCCCAAGTACCACTTCTCGTGTCAATTCATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA