Sequence
atgc intronic sequence ATGC exonic sequence...agaaattgatgatccatgattccctggattgcaatgtcaagaatttcttttattgactagtaaactaatatatcttttttacctttggttctatctttagGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATATATATGCTTGGATATGATGTGGATTTTGGTCACATGGAAGCTGTTTCTC
Basic information
species | Glycine max |
transcript | GLYMA17G05410.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 1
------agaaattgatgatccatgattccctggattgcaatgtcaagaatttcttttattgactagtaaactaatatatcttttttacctttggttctatctt-tagGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATATATATGCTTGGATATGATGTGGATTTTGGTCACATGGAAGCTGTTTCTC
|| || | || | | |||| || || | | || || | | | || || | | | | | | | |||| ||| | | || |||||||| || || || || |||||||||||||||||||||||||| || |||||||| || ||||| ||||||||| ||||||||
gccctcaggaaacggaga-----aaattcctgcgttccagaggctcaaaccactgacaggaaatttaaaccttactgaaaatcaccatgatc--taccgtcttgcagGGACTATCGCCTTATGAGAAGAAAAAGTACGTATGGAAAATGCTTTACATATATATGCTGGGTTATGATGTTGACTTTGGGCACATGGAAACTGTTTCTT
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 1
agaaattgatgatccatga--ttccctggattgcaatgtcaagaatttcttttattg--actagtaaactaata-tatcttttttacctttggttctatctt-tagGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATATATATGCTTGGATATGATGTGGATTTTGGTCACATGGAAGCTGTTTCTC
| ||| | | ||||| || || | || | |||| | ||| ||| ||| ||| | || || | ||||||| ||| ||| | ||||| ||||| || |||||||| ||||||||||||||||| |||||||| || |||||||| |||||||| || |||||| |||| ||
---agttgtaggcttgtagccctcccttgaatgttcc-tgaaacccctaaattatgggcactttgcaaccaatgctataaatcatatgatt--tcctatcttgcagGGCTTGTCACCATACGAGAAGAAAAAATATGTATGGAAAATGCTTTACATTTATATGCTGGGTTATGATGTTGATTTTGGGCATATGGAAACTGTCTCGT
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 2
-agaaattgatgatccatgattccctggat-tgcaatgtcaagaatttcttttattgactagtaaactaatatatcttttttacctttggttctatctt-tagGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATATATATGCTTGGATATGATGTGGATTTTGGTCACATGGAAGCTGTTTCTC
| | | | || || || || || | | | | | | | | || | | ||| | | || | | |||| ||| || | ||||| ||||| || |||||||| ||||||||||||||||| |||||||| || |||||||| |||||||| || |||||| |||| ||
catgcagttgtagccctccctttaatgttcctgtaaccccta-attcgtgggcactactttgcaaccaatgctataaatcatgtgatt--tcttgtcttgcagGGCTTATCACCATACGAGAAGAAAAAATATGTATGGAAAATGCTTTACATTTATATGCTGGGTTATGATGTTGATTTTGGGCATATGGAAACTGTCTCGT
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 1
agaaattgatgatccatgattccctggattg--caatgtcaagaatttcttttattg--actagtaaactaat-----atatcttttttacctttggttctatctttagGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATATATATGCTTGGATATGATGTGGATTTTGGTCACATGGAAGCTGTTTCTC
|||||||| | | | | | ||| ||| | | || | || | | |||| |||| | | |||| ||| || | | || ||| || || ||||| | || ||||||||||| |||||||||||||| ||| ||||||| || || |||||||||||||| || ||||| || |||||||
---------ggatccatgtgtggccagttggaccaacaccaaacttattttaaaatgttagaaataaattaatcatgcactcttactttaacttgttttatgttttcagGTCTTAACACCATACAAAAAGAAGAAATATGTCTGGAAAATGCTTTATATACATATGCTAGGCTACGATGTGGATTTTGGCCATATGGAGGCAGTTTCTC
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 1
agaaattgatgatccatgattccctggattgcaatgtcaagaatttcttttattgactagtaaactaatatatcttt------tttacctttggttctatcttt--agGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATATATATGCTTGGATATGATGTGGATTTTGGTCACATGGAAGCTGTTTCTC
| || ||| ||| ||| | | | || | ||| | | | || || | ||||| || || || ||| ||| ||| ||| |||||| |||||| | || ||||||||||| |||||||||||||| ||| ||||||| || || |||||||||||||| || ||||| || |||||||
------agttggaccaacattaaacttattct--ttttcggggttcatgttagaaatgaattaatcaagaactctttgattacttgacattctgttttatttttgcagGTTTTGACACCATATAAAAAGAAGAAATATGTCTGGAAAATGCTTTATATACATATGCTAGGCTACGATGTGGATTTTGGCCATATGGAGGCGGTTTCTC
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 1
agaaattgatgatccatgattccctggattgcaatgtcaagaatttcttttattgactagtaaactaatatatcttttttacctttggttctat----cttt---agGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATATATATGCTTGGATATGATGTGGATTTTGGTCACATGGAAGCTGTTTCTC
||| | | ||||| || |||| | ||||| ||||||| | | | ||| | ||| ||| || || |||| ||| |||||| |||||||| |||||||||||||| ||||||||||||||||| |||||||| || |||||||| |||||||||||||||||||| |||||||
--gcattattaacccatg-----ttgatgtgcaggctgtctaattttttttatttatttcttcttctgtatcttcctttaacccaaaatttgatggtcctttgacagGGTTTGACACCATATGAAAAAAAGAAATATGTCTGGAAAATGCTTTACATTTATATGCTGGGTTATGATGTAGATTTTGGTCACATGGAAGCAGTTTCTC
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S171_160V6.1 (Physcomitrella patens), 3'ss of exon 1
agaaattgatgatccatgattccctggattgcaatgtcaagaatttcttttattgactagtaaactaat---atatcttttttacctttggttc-tatctttagGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATATATATGCTTGGATATGATGTGGATTTTGGTCACATGGAAGCTGTTTCTC
| | || | ||| | || | | | ||| | ||| | || | ||| | | | | ||| ||| || || ||||||||||||||||| ||||| || || |||||||| |||||||| || ||||| ||||| |||||||||||| | | | |
--------------------------gcatccagtctcagggtttcgatcgttgaagtaggattctacccggagatttgattttgtggcaatccgtgcttccagGGCTTGTCTGTTTACGAGAAAAAGAAATATGTCTGGAAGATACTGTACATATACATGCTTGGGTACGATGTTGATTTCGGTCACATGGAAACAATGGCAC
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 1
agaaattgatgatccatgattccctggattgcaatgtcaagaatttcttttatt--gactagtaaactaatatatcttttttacctttggttc-tatctttagGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATATATATGCTTGGATATGATGTGGATTTTGGTCACATGGAAGCTGTTTCTC
|| ||| | | | ||| | ||||||| | ||| |||| | | ||| || | || | | ||| ||| || ||| ||||| ||||| ||||||||||| ||||| ||||| || |||||||| ||||||||||| || || ||||||||| | || |
--tttttcttgaggta-gcctgtatggcatcaaatgtcatggattgtcgaacccaagacttttcacacgcggtatgttgcaattttgccatttgtgttcccagGGCTTGTCTGTATACGAGAAGAAGAAGTATGTTTGGAAGATGCTATACATTTACATGCTTGGCTATGATGTGGACTTCGGACACATGGAAACAGTGCAAC
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ21842 (Selaginella moellendorffii), 3'ss of exon 1
agaaattgatgatccatgattccctggattgcaatgtcaagaatttcttttattgactag-taaactaatatatcttttttacctttggtt-ctatctttagGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATATATATGCTTGGATATGATGTGGATTTTGGTCACATGGAAGCTGTTTCTC
|| ||| | || || | | | | | | || || ||| | || | ||| ||||| || |||||||| || ||||| |||||||| ||||| ||||| | |||||||| |||||||| ||||| || || ||||||||||| |||
---------------------------------gtgagtgatctttttcttgctgcttgggtttcttcgtctcggattgctaagattgctcgcttgcgccagGGATTGACGCCTTATGAGAAGAAAAAATACGTTTGGAAGATGCTCTACATCTTCATGCTTGGTTATGATGTCGATTTCGGGCATATGGAAGCTGTGTCTTMapped 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|209700087|gb|BW652959.1|BW652959EST: GCGTTGACAAGGAACTCGGCAACATTCGCACGCGCTTTAAAAACGAGAAG GCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATA
genomic: GCGTTGACAAGGAACTCGGCAACATTCGCACGCGCTTTAAAAACGAGAAGgttcgcttag ... ctatctttagGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATA
EST:
gi|213597672|gb|DB964465.1|DB964465EST: GCGTTGACAAGGAACTCGGCAACATTCGCACGCGCTTTAAAAACGAGAAG GCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATA
genomic: GCGTTGACAAGGAACTCGGCAACATTCGCACGCGCTTTAAAAACGAGAAGgttcgcttag ... ctatctttagGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttattgactagtaaactaatatatcttttttacctttggttctatctttagGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATATATATGCTTGGATATGATGTGGATTTTGGTCACATGGAAGCTGTTTCTC
aactaat putative branch site (score: 2)
ttctatcttt putative PPT
tagtaaactaatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaaattgatgatccatgattccctggattgcaatgtcaagaatttcttttattgactagtaaactaatatatcttttttacctttggttctatctttagGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATATATATGCTTGGATATGATGTGGATTTTGGTCACATGGAAGCTGTTTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - tccatga
- - - - - - - - - -ttccctg
- - - - - - - - - - - - - - - -caatgtc