Sequence
atgc intronic sequence ATGC exonic sequence...aaatagaggtcatccatgtacaagtaatgacacatcaaggtccattaatagttgatcaattactatatcctacaaatctaatagattttgttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
Basic information
species | Glycine max |
transcript | GLYMA11G06250.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 3'ss of exon 5
aaatagaggtcatccatgtacaagtaatgacacatca--aggtccattaatagttgatcaattactatatcctacaaatctaatagattttgttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
| | || | | | | || || || | | | |||| | || || || || | || || | ||| ||||| ||||| |||||||||||||| || ||||| || ||||||||||| ||||||||||||||||| ||||| ||| |||| || ||||| |||
-actttctgtagtagtgaaaagaagagagaactttcgctagatttttctcgatgtgattgctgcctggataatattgtactgttgctttctgattttg-cagTCATCGGTTCTTCATTCACAACCAAAATCAACAGTTGGAACTCCAGCTTATATTGCTCCAGAAGTTTTGCTCAAGAAAGAATACGATGGAAAG
upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 5
aaatagaggtcatccatgtacaagtaatgacacatcaaggtccattaatagttgatcaa--ttactatatcctacaaatc-taatagatt-ttgttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
|| | |||| ||||| | | || | | | ||| | | ||| ||||| || ||||| ||| ||| | || | ||||||||| || || ||||||||||| || || ||||| ||||| || || |||||||| || ||||| || ||||| |||| || |||||||||
---taaatttcatttgcttacaatacactatac-tggcattactttaggacattatctggtttactctaataagcaaatgataaaagacaatctttttctgcagTCTTCAGTTCTCCATTCACAACCAAAATCCACTGTAGGAACCCCTGCTTATATTGCACCTGAAGTTCTGTTGAAGAAAGAATACGATGGCAAG
upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
aaatagaggtcatccatgtacaagtaatgacacatcaaggtccattaatagttgatcaattactatatcctacaaatctaatagatttt--gttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
| | || | || |||| | | || ||| | |||| || || | ||| ||| || ||| | || | |||||| || || |||||||| ||||| ||||||||||| ||||| || || |||||||| || ||||| || |||| |||| ||||||||||||
ggcttaatgtttacacgatagtagtagaatgatgaatatgttcat--agggttgtcagtttccttttaactaacaataccatgcattcttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 6
aaatagaggtcatccatgtacaa--gtaatgacacatcaaggtccatta-atagttgatcaattactatatcctacaaatctaatagatttt--gttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
| | || | || | ||| | | | | || | | |||| || || | ||| ||| || ||||| || | |||||| || || |||||||| || || ||||| ||||| ||||| || || |||||||| || ||||| ||| |||| |||| ||||||||||||
-----ggcttaatgtttacacgatggtagtagaataatgaatatgatcatagcgttgtcagttttcttttaactaacaataccatgcatttttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG
upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 5
-------aaatagaggtcatccat--gtacaagtaatgacaca-tcaaggtccattaatagt--tgatcaattactatatcctacaaatctaata--gattttgttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
|||| | || | ||| || || | ||| | ||| | | || || || |||| | | | | | | | | | ||| || ||| |||||||| || |||||||||||||| ||||||||||| || ||||| ||||| || |||||||| ||| |||| || || ||||||||||||
gtatcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatg-tgtttttaaagtgtttgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG
upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
-----aaatagaggtcatccatgtacaagtaatgacacatcaaggtccattaatagttgatcaattactatatcctacaaatctaatagat-tttgttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
| | | | | |||| || | | | | ||| || || ||| || | | || | || ||| || | |||||||| || |||||||| ||||| ||||||||||| || ||||| ||||| ||||| ||||| | | || || || ||||||||||||
tcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctt---tgatttctg---ctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------------------------------------aaatagaggtcatccatgtacaag-taatgacacatcaaggtccattaatagttgatcaattac----tatatcctacaaatctaatagat-----tttgttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
| | | | | || || | | | || | || || || || || | | | || | | || || | ||| || | |||||||| || |||||||| ||||| ||||||||||| || ||||| ||||| ||||| ||||| | | || || || ||||||||||||
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
---aaatagaggtcatccatgtacaagtaatgacacatcaaggtccat-taatagttgatcaattactatatcctacaaatctaatagattttgttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
| | | ||| | | | ||| | | | | || || | || | | |||| ||| | || ||||||| | || | | || |||||||||||||||||||||||||| || |||||||| |||||||| ||||| ||||||||||||||||| ||| |||||| || |||||||||
agcatctgtacatcagcattcaatgggtattcaatcccctttgttcacgttatcctaggatcattattatttgct-caaatctgacag---tggcacttctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAG
upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S113_72V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------aaatagaggtc-atccatgtacaagtaat--gacacatcaaggtccattaatagttgatcaattactatatcctacaaatct--aatagattt--tgttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
|||| | || | | | | ||| | || || || | | | | | || || ||| || || | || | ||| |||| | ||||| || || | || || ||||||||||| || |||||||| || || || ||||||||||| || ||| |||| ||||||| |||||||||
gtgtgttgctttaatatctttcaattggtccactggaagctggatagtgttctagttgtattgatgtagttcgattgattgagcactgtgatttatctat--atgactcagcactgcagtttctgaaccgctttcgtgttgattccagTCCTCTTTGTTGCACTCCCAACCTAAGTCGACCGTGGGAACCCCCGCTTACATTGCTCCAGAGGTCTTGTCGAAGAAAGAGTACGATGGCAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|9258485|gb|BE346632.1|BE346632EST: ATGGAAGCCCGGCACTTCATTTGAAGATATGTGATTTTGGATACTCCAAG TCTTCGGTGCTTCATTCACAACCTAAGTCAACCTGTGGGA-CTCCAGCATA
genomic: ATGGAAGCCCGGCACTTCATTTGAAGATATGTGATTTTGGATACTCCAAGgtaagtgttt ... ttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAAC-TGTGGGAACTCCAGCATA
EST:
gi|254317661|gb|GR826645.1|GR826645EST: ATGGAAGCCCGGCACTTCATTTGAAGATATGTGATTTTGGATACTCCAAG TCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATAT
genomic: ATGGAAGCCCGGCACTTCATTTGAAGATATGTGATTTTGGATACTCCAAGgtaagtgttt ... ttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatagttgatcaattactatatcctacaaatctaatagattttgttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
atctaat putative branch site (score: 3)
ttttgtt putative PPT
aaatctaatagatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatagaggtcatccatgtacaagtaatgacacatcaaggtccattaatagttgatcaattactatatcctacaaatctaatagattttgttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - -tcatcca
- - - - - - - - - - - - - - - cacatca
- - - - - - - - - - - - - - - - - - - - -ccattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctaca