Sequence
atgc intronic sequence ATGC exonic sequence...tagaattgtctagctttatcatgtactttttctgttttgctttacagatttcctgtattatcttttttctgtcacatttatatttggttttcattttcagTGCTCCAATAGGTCAAGGATATGGTCTAACAGAGACTTGTGCTGGTGGGTCATTCTCTGATTTTGACGATACATCTGTTGGACGTGTTGGGCCACCTGTT
Basic information
species | Glycine max |
transcript | GLYMA06G11860.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------------tagaattgtctagctttatcatgtactttttctg-ttttgctttacagatttc---------ctgtattatcttttttctgtca----catttata---tttggttttcatttt--cagTGCTCCAATAGGTCAAGGATATGGTCTAACAGAGACTTGTGCTGGTGGGTCATTCTCTGATTTTGACGATACATCTGTTGGACGTGTTGGGCCACCTGTT
||||| | | | ||| || | || || ||| ||| ||| || || | |||| || ||| | | ||||| || | | ||| ||||||||||| |||||||||||||| || || || |||||||| ||| |||| || || | ||| || | |||||||| |||||||| | || |
gtgagatagtactcttcattattttataagccattctcaagtctcttttgttaatatcaagttattgtttttggtccacttgtgtttactgtgattgaacttcacaatattcaaatctaacttgcatactgcattttaaaccaaaacaattgacaggttttgggttgtgctgttgcagGGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGACATTTTCCGAGTATGATGACAATTCTGTTGGCCGTGTTGGTGCTCCATTG
upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 7
----------------------------------------------tagaattgtctagctttat--catgtactttttctgttttgctttacagatttcctgtattatcttttttctgtcacatttatatttggttttcattttcagTGCTCCAATAGGTCAAGGATATGGTCTAACAGAGACTTGTGCTGGTGGGTCATTCTCTGATTTTGACGATACATCTGTTGGACGTGTTGGGCCACCTGTT
| ||| | | || |||| | || | | | | | | | | | | ||| | | ||||| ||| | | || |||||| ||||||||||| ||||| |||||||| || || ||||||||||| ||| |||| || || | ||| || |||||||| || |||||||| | || |
gtaagattatgtatgcctcatttctgttgtttgatggcaattatcttgaaatcctatgttcccatcgcatgcatttaatacgataaatatgttatgacttcctcactgtgtttgcagtctgacattgataaggtttatgcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA
upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 7
---tagaattgtctagctttatcatgtactttttctgttttgctttacagatttcctgtattatcttttttctgtcacatttatatttggttttcattttcagTGCTCCAATAGGTCAAGGATATGGTCTAACAGAGACTTGTGCTGGTGGGTCATTCTCTGATTTTGACGATACATCTGTTGGACGTGTTGGGCCACCTGTT
| | | || | | || | | || || | | | || | ||| | || | ||||| | || || || | ||| |||| |||||||| ||||| |||||||| || |||||||||||||||||||| | ||||| || ||||| || ||||| ||||| |||||||| | || ||
gtaaacgaatccctgaatatctccttgaggcttgctactctccaatatatcttttc-gtccctttccatttctatg--atctaacactgatattc---ctcagGGCTCCAATCGGTCAGGGATATGGGCTCACAGAGACTTGTGCTGGTGGAACCTTCTCGGAGTTTGAGGACACATCCGTTGGCCGTGTTGGTGCTCCACTT
upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 8
tagaattgtctagctttatcatgtactttttctgttttgct-ttacagatt-tcctgtattatcttttttct-gtcacatttatatttggt----tttcattttcagTGCTCCAATAGGTCAAGGATATGGTCTAACAGAGACTTGTGCTGGTGGGTCATTCTCTGATTTTGACGATACATCTGTTGGACGTGTTGGGCCACCTGTT
| || | | || ||| | | | | | | | | ||||||| || ||| || | || | || | ||||||||||||||||||||| |||||| ||||| || ||||||| |||||||||||| |||| || || | ||| |||||||||||||| |||||||| | || ||
-------atttaaggaaacacttagctggcaatgtcctacaatcatgcagtatgcaatattatccttcctcttgttgtaattgctctaagtgaactgtcattttcagTGCTCCAATAGTTCAAGGGTATGGCCTGACAGAGAGTTGTGCTGGTGGTACATTTTCCGAGTATGATGATACATCTGTTGGTCGTGTTGGTGCTCCACTT
upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S15_17V6.1 (Physcomitrella patens), 3'ss of exon 6
----tagaat-tgtctagctttatcatgtactttttctgttttgctttacagatttcctgtattatcttttttctgtcacatttatatttggttttcattttcagTGCTCCAATAGGTCAAGGATATGGTCTAACAGAGACTTGTGCTGGTGGGTCATTCTCTGATTTTGACGATACATCTGTTGGACGTGTTGGGCCACCTGTT
| || |||| | || | || | | || | ||| ||| || ||| | | | | |||| | | ||| ||| |||| |||||||| |||||| ||||||||||||||||||||||| ||||| | || | || ||| || ||| | |||| ||||| ||
tccacggcatgtgtcagtgtgtacaactcggttcactcggtctgatgccacgatgctctgg--taccttaacttaagaaactgcgtg---ggttattttcggcagAGCTACAATCGGTCAAGGCTATGGTTTAACAGAGACTTGTGCTGGTGGGACATTCACCGAATGGGATGATCGCTCCGTTCGTCGTGCGGGGCCTCCGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatttcctgtattatcttttttctgtcacatttatatttggttttcattttcagTGCTCCAATAGGTCAAGGATATGGTCTAACAGAGACTTGTGCTGGTGGGTCATTCTCTGATTTTGACGATACATCTGTTGGACGTGTTGGGCCACCTGTT
ttttcattttc CT-rich tract
atttatatttggtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagaattgtctagctttatcatgtactttttctgttttgctttacagatttcctgtattatcttttttctgtcacatttatatttggttttcattttcagTGCTCCAATAGGTCAAGGATATGGTCTAACAGAGACTTGTGCTGGTGGGTCATTCTCTGATTTTGACGATACATCTGTTGGACGTGTTGGGCCACCTGTT
- - - - - - - - - -catgtac
- - - - - - - - - - - - - - - - tgttttg