Sequence
atgc intronic sequence ATGC exonic sequence...ttaattttcttgcataaattaattggctaattatgtttttttgggggtgtgttaaatttcctatttgttggagtgatggaattttatttgttggttacagAGACCACAACTTGTAAAAGGAAATATGCAACTCTTCTCTGTGGATCAGCAGAGGAGCCAGGCTCTTGAAGCACATGCTGCCTCATTTGCCACATTTAGG
Basic information
species | Glycine max |
transcript | GLYMA01G38580.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 5
ttaattttcttgcataaattaattggctaattatgtttttttgggggtgtgttaaatttcctatttgttggagtgatggaattttatttgttggttacagAGACCACAACTTGTAAAAGGAAATATGCAACTCTTCTCTGTGGATCAGCAGAGGAGCCAGGCTCTTGAAGCACATGCTGCCTCATTTGCCACATTTAGG
|| | | || | | | |||| || | || || | | | | | ||||| | | ||| ||||| |||||||| || || |||||||||||||| || |||||||||||||| | || ||||| |||||||| ||||| || || ||||| |||||| |
atatgctacacctatgctggagcagttcttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 5
ttaattttcttgcataaattaattggctaattatgtttttttgggggtgtgttaaatttcctatttgttggagtgatggaattttatttgttggttacagAGACCACAACTTGTAAAAGGAAATATGCAACTCTTCTCTGTGGATCAGCAGAGGAGCCAGGCTCTTGAAGCACATGCTGCCTCATTTGCCACATTTAGG
|| | | || || | | | |||| || | || || | | | | | ||||| | | ||| ||||| |||||||| || || |||||||||||||| || |||||||||||||| | || ||||| |||||||| ||||| || || ||||| |||||| |
atatgctacacctatgctggaacagtttttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 4
---------ttaattttcttgcataaattaattggctaattatgtt-tttttgggggtgtgttaaatttcctatttgttggagtgatggaattttatttgttggttacagAGACCACAACTTGTAAAAGGAAATATGCAACTCTTCTCTGTGGATCAGCAGAGGAGCCAGGCTCTTGAAGCACATGCTGCCTCATTTGCCACATTTAGG-
|| ||||| | | ||||| | |||||| | || | || ||| | || ||||||| ||| | | |||| | |||||||||||||| || || |||||||||||||| || ||||| ||||| ||| | |||||||| |||||||| ||||| || || ||||| ||||||| |
cggactaaaagaaatttctgtaagtcagtaattag-taattacacaatactttgttgtatgt-gcttctcatatttgt-------atgccctcct-tttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAGG
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
---------ttaattttcttgcataaattaattggctaattatgtttt-tttgggggtgtgttaaatttcctatttgttggagtgatggaattttatttgttggttacagAGACCACAACTTGTAAAAGGAAATATGCAACTCTTCTCTGTGGATCAGCAGAGGAGCCAGGCTCTTGAAGCACATGCTGCCTCATTTGCCACATTTAGG
|| ||||| | | ||||| | |||||| | || | || ||| | || ||||||| ||| | | |||| | |||||||||||||| || || |||||||||||||| || ||||| ||||| ||| | |||||||| |||||||| ||||| || || ||||| ||||||| |
cggactaaaagaaatttctgtaagtcagtaattag-taattacacaatactttgttgtatgt-gcttctcatatttgt-------atgccctcct-tttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 5
ttaattttcttgcataaattaattggctaattatgtttttttgggggtgtgttaaatttcctatttgttgga-gtgatggaattttatttgttggttacagAGACCACAACTTGTAAAAGGAAATATGCAACTCTTCTCTGTGGATCAGCAGAGGAGCCAGGCTCTTGAAGCACATGCTGCCTCATTTGCCACATTTAGG
| | ||| | ||| | | || | | || | |||| || | | || | | || | | ||||| |||| |||||||| || ||||| ||||||||||| ||||| ||||||||||| | || ||||| ||||||||||||||||| ||||||||| ||||||
aggacctgctt-tttcaatgagcattgcatgtagcctaacaacagcgtaaaattgattttttaacaatgatatatgttccatcttaaaattgtggttgtagAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 3'ss of exon 5
ttaattttcttgcataaattaattggctaattatgtttttttgggggtgtgttaaatttcctatttg---ttggagtgatggaattttatttgttggtta-cagAGACCACAACTTGTAAAAGGAAATATGCAACTCTTCTCTGTGGATCAGCAGAGGAGCCAGGCTCTTGAAGCACATGCTGCCTCATTTGCCACATTTAGG
|| | || || ||| ||| | | || | || || | |||| |||| || | ||| | || || ||||| ||| | || |||||||| |||||||| ||||| | || || ||||| ||||||||||| ||||| |||||||| |||||||| |||||||| | |
---atctctcctcagcaacctcttgaaattttaattatcgtttagagt-tggttcctttctcatttaacactgcattgacagttcttatttctctggttttcagCGGCCCCAACTTGTGAAAGGAAACATGCAGTTGTTTTCAGTGGACCAGCAGAGGAGTCAGGCGCTTGAAGCTCATGCTGCGTCATTTGCTTCCCACCAG
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 5
ttaattttcttgcataaattaattggctaattatgtttttttgggggtgtgttaaatttcctatttgttggagtgatggaattttatttgttggttacagAGACCACAACTTGTAAAAGGAAATATGCAACTCTTCTCTGTGGATCAGCAGAGGAGCCAGGCTCTTGAAGCACATGCTGCCTCATTTGCCACATTTAGG
| | ||| || || |||| | | | | | | || | | || || | |||||||| || |||||||| ||||||||||| || || ||||||||| | || || ||| | ||||| |||||||| || || || ||||| | |
--------------------------------gtatccattt-----cttgaaaagtttcttgtagct---aacaaagaaactctttt----------agCGTCCACAACTGGTGAAAGGAAACATGCAACTCTTTTCAGTCGATCAGCAGCGAAGTCAAGCTTTGGAAGCTCATGCTGCATCTTTCGCTACATTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtgtgttaaatttcctatttgttggagtgatggaattttatttgttggttacagAGACCACAACTTGTAAAAGGAAATATGCAACTCTTCTCTGTGGATCAGCAGAGGAGCCAGGCTCTTGAAGCACATGCTGCCTCATTTGCCACATTTAGG
ttaaatttcctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaattttcttgcataaattaattggctaattatgtttttttgggggtgtgttaaatttcctatttgttggagtgatggaattttatttgttggttacagAGACCACAACTTGTAAAAGGAAATATGCAACTCTTCTCTGTGGATCAGCAGAGGAGCCAGGCTCTTGAAGCACATGCTGCCTCATTTGCCACATTTAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - tgcataa
- - - - - - - - - - - - - - - - - - - - - - gggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgatgg