Sequence
atgc intronic sequence ATGC exonic sequence...tcccgaagcttacatttttgtgttatttaaatttctgaacatcaaaccttgtgagattattaattgtaagaataattttatcacattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCATTTGCTTCGTTTAGA
Basic information
species | Glycine max |
transcript | GLYMA14G37510.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 5
--tcccgaagcttacatttttgt-gttatttaaatttctgaacatcaaaccttgtgagattattaattgtaagaataattttatcacattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCATTTGCTTCGTTTAGA
| | | || | | ||| || ||| || || | | | |||| || | || ||| | | || | || | |||| | |||| |||||||| || || ||||| |||||||| || |||||||||||||||||||||||||| |||||||| ||||| || || ||||| || ||||
atatgctacacctatgctggagcagttcttaaaagtttattacgtaatgctttgttctata--tcatcctaacattgatgtgctctctttttcacccat-cagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 5
--tcccgaagcttacatttttgt-gttatttaaatttctgaacatcaaaccttgtgagattattaattgtaagaataattttatcacattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCATTTGCTTCGTTTAGA
| | | || | ||| || ||| || || | | | |||| || | || ||| | | || | || | |||| | |||| |||||||| || || ||||| |||||||| || |||||||||||||||||||||||||| |||||||| ||||| || || ||||| || ||||
atatgctacacctatgctggaacagtttttaaaagtttattacgtaatgctttgttctata--tcatcctaacattgatgtgctctctttttcacccat-cagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 4
--tcccgaagcttacatttttgtgttatttaaatttctgaacatcaaaccttgtgagattattaattgtaagaataattttatcacattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCATTTGCTTCGTTTAGA-
| || | | | | || | | |||| | | | || | || | | || | | | | | | | | ||||| ||||||||||||| || || ||||| |||||||| || ||||| ||||| || ||||| ||||| |||||||| ||||| || || ||||| | ||||
cggactaaaagaaatttctgtaagtcagt--aattagtaattacacaatactttgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAGG
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
--tcccgaagcttacatttttgtgttatttaaatttctgaacatcaaaccttgtgagattattaattgtaagaataattttatcacattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCATTTGCTTCGTTTAGA
| || | | | | || | | |||| | | | || | || | | || | | | | | | | | ||||| ||||||||||||| || || ||||| |||||||| || ||||| ||||| || ||||| ||||| |||||||| ||||| || || ||||| | ||||
cggactaaaagaaatttctgtaagtcagt--aattagtaattacacaatactttgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 5
tcccgaagcttacatttt---tgtgttatttaaatttctgaacatcaa-accttgtgagattattaattgtaagaataattttatcacattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCATTTGCTTCGTTTAGA
| | | |||| || | | | | | |||| || | || |||| | | | || ||| | | | ||||||||| |||||||| || ||||| || |||||||| ||||| ||||||||||||||||||||||| ||||||||||||||||| |||||||| || |||| |
----aggacctgctttttcaatgagcattgcatgtagcctaacaacagcgtaaaattgattttttaacaatgatatatgttccatcttaaaattgtggttgtagAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 3'ss of exon 5
---tcccgaagcttacatttttgtgttatttaaatttctgaacatcaaaccttgtgagattattaattgtaagaataattttatcacattttgtttgttgt-agAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCATTTGCTTCGTTTAGA
|| | || | || || | || | | | | | | ||| | || | | | || | |||| | ||| | || | || ||||| || |||||||||||||| | || || ||||| ||||| | |||||||| |||||||| |||||||| |||||||||||
atctctcctcagcaacctcttgaaattttaattatcgtttagagttggttcctttctcatttaacactgcattgacagttct----tatttctctggttttcagCGGCCCCAACTTGTGAAAGGAAACATGCAGTTGTTTTCAGTGGACCAGCAGAGGAGTCAGGCGCTTGAAGCTCATGCTGCGTCATTTGCTTCCCACCAG
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 5
tcccgaagcttacatttttgtgttatttaaatttctgaacatcaaaccttgtgagattattaattgtaagaataattttatc--acattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCATTTGCTTCGTTTAGA
| ||| ||| || | || || | ||| | || ||| | |||||||| || |||||||||||||||||||| || || |||||||| || ||||| ||| | ||||| |||||||| || || ||| | || |
----------------------------------------------------gtatccatttcttgaaaagtttcttgtagctaacaaagaaactcttttagCGTCCACAACTGGTGAAAGGAAACATGCAACTCTTTTCAGTCGATCAGCAGCGAAGTCAAGCTTTGGAAGCTCATGCTGCATCTTTCGCTACATTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accttgtgagattattaattgtaagaataattttatcacattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCATTTGCTTCGTTTAGA
tattaat putative branch site (score: 2)
ttttgttt putative PPT
attattaattgtaaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcccgaagcttacatttttgtgttatttaaatttctgaacatcaaaccttgtgagattattaattgtaagaataattttatcacattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCATTTGCTTCGTTTAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - -gcttaca
- - - - - - - -ttttgtg
- - - - - - - - - - - - - - - - -tctgaac
- - - - - - - - - - - - - - - - - - - - -tcaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaataa