Sequence
atgc intronic sequence ATGC exonic sequencegtaactttctgcttgcttgttaaacgttaattttttacactcaatttattattaactttattatttccttgatctgtttgttcagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG
Basic information
species | Glycine max |
transcript | GLYMA01G43910.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G011518_T04 (Zea mays), 3'ss of exon 1
-------gtaactttctgcttgcttgttaaacgttaa----------ttttttacactcaatttattattaactttattatttccttgatctgtttgttcagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG---------
|| || | | | | | ||| ||||| || || | ||| | ||| ||| || | ||| |||||| ||||||||||| | ||||| ||||| ||||| || ||||| || ||| |||||||||| |||||| | ||||| || ||||| || |
atgtttagtcttctttttttatatcatcggagattagaaccagtatccgttttaagctgaacatgcctctaa-tagattggcctctt-atttttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAGGTCCGATTG
upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 1
-------gtaactttctgcttgcttgttaaacgttaa----------ttttttacactcaatttattattaactttattatttccttgatctgtttgttcagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG
|| || | | | | | ||| ||||| || || | ||| | ||| ||| || | ||| |||||| ||||||||||| | ||||| ||||| ||||| || ||||| || ||| |||||||||| |||||| | ||||| || ||||| || |
atgtttagtcttctttttttatatcatcggagattagaaccagtatccgttttaagctgaacatgcctctaa-tagattggcctctt-atttttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAG
upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G113995_T03 (Zea mays), 3'ss of exon 1
-------------------gtaactttctgcttgcttgttaaacgttaattttttaca------ctcaatttattattaactttattatttccttg-atctgtttgttcagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG
| | ||| | ||| ||| || | ||| ||| || || ||| ||| || ||| | ||| || ||||| ||||||||||||||||||| |||||||| || ||||| || ||| | |||||| | || || || || ||||| || || ||||| || ||||
gtctgctcatatttttgccgcgatttttctttcgctatttagttgt--actttctacgaactgcctgtatgtatcattttgttgattgtggttttgtgcttgcttgtt-agGTTGTGATGCTTGGTCTGGATGCTGCCGGTAAAACCACCATATTGTACAAGCTGCATATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG
upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 2
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------gta-actttctgcttgcttgttaaacgttaattttttacactcaatttattattaactttattat-ttccttgatctgtttgttcagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG
|| ||||| || | | | | | | | | |||| | | ||| || | || ||| | || ||||| || ||||| ||||| ||||| |||||||||||||| ||||| |||||| | ||||| ||||||||| | || || ||||| ||||| |
actaatctatgtggtgtggtttctcactgtgcatgatatgatgaatacatttttcagatttggtgatttttttcttgtgttttttgttttgagatgccagGTCGTTATGCTGGGTCTGGATGCGGCTGGCAAAACAACGATACTATACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCG
upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 1
-----gtaactttctgcttgcttgttaaacgttaatt-----ttttacactcaatttattattaactttattatttccttgatctgtttgtt-----cagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG
|| ||| | || ||| | | | | | || | | |||| | | | || | || ||| || | | || ||||| || ||||| || || ||||||||||| ||||||||||| || |||||| |||| |||||||||||||| || || ||||| || ||||
gaatcatagatttgttgttagctgtggcatgatgaatcagaattgaagaaatgatttttgaatctctcttttttttttccaattttgtgattaatgacagGTCGTTATGCTGGGGCTGGATGCTGCTGGAAAAACAACTATTCTCTACAAGCTTCATATTGGAGAAGTTTTGTCTACTGTTCCCACCATTG
upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 1
-----gtaactttctgcttgcttgttaaacgttaattttttaca-ctcaatttattattaactttattatttccttgatctgtttgtt---------cagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG
| | ||| ||| || | | || || ||| | | ||| || | | | ||| || || || | | || || |||||||||||||||| || ||||| ||||| |||||||| ||||| ||||| || ||||||||||||||||| ||||| ||||| |||||||
tattcttgagtttatgcctgtattcttaatatttattcatgatttctctatgtccttcgagcttattttcttatttaaattattaattgagttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAATTGCACATTGGAGAAGTTTTGTCCACTGTTCCCACAATTG
upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 1
--------gtaactttctgcttgcttgttaaacgttaattttttacactcaatttattatta-actttatt---atttcct-tgatctgtttgtt---cagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG
| | | || || ||| | |||| |||| | ||| | |||| ||||| | ||| | | | |||||||||||||||||| | ||||| || |||||||| || || || || ||| ||||||||||||| || | ||||||||||| || ||||
gttcatctacatttgaatcgatgttttttagatag-aattccatacaggaagcacattcctgtgatttaccgagatttcttacgattcttgtatctgccagGTTGTGATGCTTGGTTTAGATGCAGCAGGCAAAACCACCATCCTCTATAAGCTTCACATTGGAGAGATTCTGTCCACCGTTCCCACCATTGMapped 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|151393667|gb|EV263542.1|EV263542EST: CTTTTCGAAAGCTCTTTGACACCTTCTTCGGCAACACCGAGATGAGG GTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAG
genomic: CTTTTCGAAAGCTCTTTGACACCTTCTTCGGCAACACCGAGATGAGGgtaactttct ... gtttgttcagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttacactcaatttattattaactttattatttccttgatctgtttgttcagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG
tctgttt CT-rich tract
tacactcaatttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactttctgcttgcttgttaaacgttaattttttacactcaatttattattaactttattatttccttgatctgtttgttcagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT