Sequence
atgc intronic sequence ATGC exonic sequence...tggaaagaaagacaaaaatatttgttaactatgaaggttataatgcttcttgagtttttgtaacatgaactagttaacatatattggtgcttctttgcagATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
Basic information
species | Glycine max |
transcript | GLYMA08G17140.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g33940.1 (Oryza sativa), 3'ss of exon 2
----------------------------------tggaaagaaagacaaaaatatttgttaactatg-aaggttataatgcttcttgagtttttgtaacatgaactagttaacatatattggtgcttctttgcagATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
|| || | | | || ||| || | || || ||||| |||||| | |||| || | || | | | | ||||| ||| ||||| ||| | ||||||||||| |||||||| ||||||||||||||||||||||||||||| || || || || || ||||| || || ||
gtaaaattgaaattgagcaatcaatcagtcagctcatctagctagccggccggagctagcaagcatgcaacagtgagatttagctgaagttta---aacatgg--tgattaatatttcatgtggtatatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACCGGGCGACGAC
upper sequence: GLYMA08G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------tggaaagaaagacaaaaatatttgtt------------aactatg-----aaggtta--taatgcttcttgagtt---tttgtaacatgaactagttaacatatat-tggt-gcttctttgcagATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
|| | | | ||||| ||| |||| || | | || | | ||| | || | | || ||| | | || | | ||||||||||| |||| || | ||||||| || ||||||||| | ||| | ||| | |||||||| ||||||||||||||||||||||||||||| || || || || || ||||| || ||
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatga-atatattgattaacatatatatggttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
upper sequence: GLYMA08G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G104074_T01 (Zea mays), 3'ss of exon 2
tggaaagaaagacaaaaatatttgttaactatgaaggttataatgcttcttgagtttttgtaacatgaactagttaa--catatattggtgcttctttgcagATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
| ||| | | ||| | | || ||||||| || | | | ||| | ||||||| ||| | ||||| | || | || || | |||||||| || |||||||| |||||||||||||||||||||||||||||||| ||||| ||||| ||||| || || ||
--tttaaaaatatatgaatctaaagccaaaatatctcttataatttgaaaagaagtatataggtaactcataggaaggttatatatttgtggacaatggcagAAAGATGCAAAATAGGCACTGGGCCTCAAAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACGGGAACGAGAACGAACCGTGCCACGAC
upper sequence: GLYMA08G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------------tggaaagaaagacaaaaatatttgttaacta--tgaaggttataatgcttcttgagtttttg---------taacatgaactagttaacatatat-tggtgc-----ttctttgcagATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
|| | || | | ||| || ||| | | | || | || ||| | | ||| || | | |||||| ||| | | | | ||||| | ||| ||||| || | |||| |||||| |||||||| ||||||||||||||||||||||||||||| || ||||| || || ||||| || || ||
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
upper sequence: GLYMA08G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G155816_T01 (Zea mays), 3'ss of exon 2
tggaaagaaagacaaaaatatttgttaactatgaaggttataatgcttcttgagttt-ttgtaacatgaactagttaacatatatt---ggtgcttctttgcagATAAGTGTAGGATTGGGTC---AGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
| ||| || | | ||| | || | | || | ||| | | | | | | || || | || |||| | |||||| ||| ||||||||| | | ||||||| | |||||||||||||||||||||||||||| ||||||||| || || || |||| ||||| || ||
----gtaactgactaata-acttgaatgcggtgtac-tagtagaaatctaagagctaataatgtctagtgtttcacaatatgtgttcatggtggacgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCAGCCACAAGGACAGGAAGTACCCTACGGGGACGCGAACCAACCGGGCGAC---
upper sequence: GLYMA08G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G79580.1 (Arabidopsis thaliana), 3'ss of exon 2
tggaaagaaagacaaaaatatttgttaactatgaaggttataat-gcttcttgagtttttgtaacatgaacta-gttaacatatattggtgcttctttgcagATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
|| | | | | |||| | | ||| ||| |||||| ||| ||||| || | || || | | ||| || | | || ||| || || || || ||||| || ||||| || |||||||||||||| ||||||||||||||||| || || || || ||| |||| ||||| || || |
tgtgtgtttaaatatatatatatatatactt--aagactataattaacaattgtattttttcaattatatttataacaaattttgttgttgtgtgtatgtagAGAAATGCAGAATCGGGTCGGGTCCTCAAAACGAGTGGTATTTCTTTAGCCACAAGGACAAGAAATATCCGACTGGGACCCGAACGAACCGGGCGACAGC
upper sequence: GLYMA08G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0085g01210.t01 (Vitis vinifera), 3'ss of exon 1
tggaaagaaagacaaaaatatttgttaactatgaaggttataatgcttcttgagtttttgtaacatgaactagttaacatatattggt---gcttctttgcagATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
| || | |||| | | | | || || ||| | ||| ||| | || | | | | | | | | ||||||||| || | ||||| ||||| ||||||| |||||||||||||||||||||||||| ||||| |||||||| ||||| |||||||||||||||| |
--actaatcagtccgcaatacccaaaagcaagattaaagttgata-ttattgcagtacggtattgggaaatttttcatgtttttggatttggttggcatgcagATAAATGCCGAATTGGATCAGGCTCTCAGAACGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATACCCAACTGGAACTCGAACAAACCGAGCAACCAT
upper sequence: GLYMA08G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------------tggaaaga-aagacaaaaatatttgtt-aactatgaaggttataa-------------tgcttcttgagtttttgtaacatgaactagttaacatatattgg--------tgcttctttg--cagATAAGTGTAGGATTGGG---------TCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
| | | || ||| | ||| || || | ||| |||| | || || | || || |||||| | || | ||||| || | | | |||| ||| ||||| ||| ||| || ||| | ||| ||||| ||||||||||||||||| |||||||| || ||||||| | | | |||||
gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataagctcaagagcatgttctcctcatctattgatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG---------
upper sequence: GLYMA08G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
-----------------------tggaaagaaagacaaaaatatttgttaactatgaaggttataatgcttcttgagtttttgtaacatgaactagttaacatatattggtgcttctttgcagATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
| | || ||||| | ||| || || | || | | |||| | | | | | | | || | | |||| ||| | ||||| || | | ||| | |||||||| |||||||||||||| |||||||| ||||| || || || || || ||| |||| ||
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgtt--ctttggaagtctttgcg-ttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: GLYMA08G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
------------------------tggaaagaaagacaaaaatatttgttaactatgaaggttataatgcttcttgagtttttgtaacatgaactagttaacatatattggtgcttctttgcagATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
| || ||||| | ||| || || | || | | |||| | | | | | | | || | | |||| ||| | ||||| || | | ||| | |||||||| |||||||||||||| |||||||| ||||| || || || || || ||| |||| ||
gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaaccgtt--ctttggaagtctttgcg-ttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGGMapped 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|254317458|gb|GR826442.1|GR826442EST: TGTCATAAGAGAAGTAGATCTCAACAAACTTGAGCCTTGGGACCTCAATG ATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCC
genomic: TGTCATAAGAGAAGTAGATCTCAACAAACTTGAGCCTTGGGACCTCAATGgtacacaaca ... ttctttgcagATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcttgagtttttgtaacatgaactagttaacatatattggtgcttctttgcagATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
tgcttcttt CT-rich tract
tagttaacatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggaaagaaagacaaaaatatttgttaactatgaaggttataatgcttcttgagtttttgtaacatgaactagttaacatatattggtgcttctttgcagATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- -aaagaaa
- - - - - - -aaaaata
- - - - - - - - - - - - - - -tatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttggtgc