Sequence
atgc intronic sequence ATGC exonic sequencegtaactaactacattcagctattcatctttgtcacttaagatgcgaatgctctacagaataatgggattagataattacattatctttatacactgtagGAAATATGGGATGAGGTTGGTGAGAGCGATGAGCAACGAGACAAGATGCTTCTTCAGTTAGAACAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
Basic information
species | Glycine max |
transcript | GLYMA02G46450.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G46450.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------gtaactaactacattcagctattcat-ctttgtcacttaagatgcgaatgctctacagaata----atgggattagataattacattatctttatacactgtagGAAATATGGGATGAGGTTGGTGAGAGCGATGAGCAACGAGACAAGATGCTTCTTCAGTTAGAACAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
| || | | | | |||| | | | || | | |||| | || || || ||||| || || | | | | | || | || |||||||||||||||||||| |||||||| | || ||||||||| | |||||| ||||||| || ||||||||||| |||| |||||||||||| |
gtgcctttgtctcttccaatgttcttttgtatgtgtgctttataatgactggaactaaggatagcagcaagccattttagttccctatctacaccatagcatctgtgcaacgaaaagttatatgagtagtgcataggattggacaagtgactgactagtgt-catttcagTTGATATGGGATGAGGTTGGTGAAAGCGATGAAGACCGTGACAAGATGTTACTTCAGCTAGAACAAGAATGCTTGGATGTTTACAGGAGAAAGGTTGATC
upper sequence: GLYMA02G46450.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g20370.1 (Oryza sativa), 3'ss of exon 2
--------gtaactaactacattcagctattc-atctttgtc-acttaagatgcgaatgctctacagaataatgggattagataattacattatctttatacactgtagGAAATATGGGATGAGGTTGGTGAGAGCGATGAGCAACGAGACAAGATGCTTCTTCAGTTAGAACAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
| | | | | | | | | ||| ||| | || | ||| | | | || ||| | | | ||| | |||| || ||||||||||| |||||||||||||| ||| | || |||||| | || |||||||| ||||||||| ||||||| |||||||| || ||||| |
gtgcgtgattgatttgttgcttgtgcttttgcgatccgcgtctagtttatgcatttgtgccttgctttgtgttgtgatagtggtgtgcttctgttcttaaa-actgcagTTGATATGGGATGAAGTTGGTGAGAGCGACGAGGACCGCGACAAGGTCCTGTACCAGTTAGATCAGGAGTGCCTGGATGTTTACAAGAGGAAAGTTGACC
upper sequence: GLYMA02G46450.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G112337_T02 (Zea mays), 3'ss of exon 4
gtaactaactacattcagctattcatct---ttgtcacttaagatgcgaatgctctacagaataatgggattagataattaca--ttatctttatacactgt---agGAAATATGGGATGAGGTTGGTGAGAGCGATGAGCAACGAGACAAGATGCTTCTTCAGTTAGAACAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
||| | | | | ||| |||| || | ||||||| | | || | || | | | || ||| ||| | || ||| | | || ||||||||||||||||| || || ||||| | || ||||||||| | |||||| |||| || |||||||| ||||| || | |||||||||||| |
------aaccattctaacccatt-atctagattaagagttaagatagcatttctacaagaaagagtagtataggattcacacaagtgattgctatgtgttatttcagCTGATATGGGATGAGGTTGGCGAAAGTGATGAAGATCGTGACAAGATGTTACTTCAGCTAGAGCAAGAGTGCTTAGATGTTTATAGGAGAAAGGTTGATC
upper sequence: GLYMA02G46450.3 (Glycine max), 3'ss of exon 2
lower sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaactaactacattcagctattcatctttgtcacttaagatgcgaatgctctacagaataatgggattagataattacattatctttatacactgtagGAAATATGGGATGAGGTTGGTGAGAGCGATGAGCAACGAGACAAGATGCTTCTTCAGTTAGAACAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
|| || |||| ||||| ||| |||| | | ||| ||| | || ||| || | ||| | ||| ||||||| |||||||| ||||||||||| ||||| |||||||||| ||||||||||| |||| || ||||| | || || ||||||||||| || ||||
--------gtaaatcttgctac-catctc---cacctaag-tattagggctttac----tctcaatcttgtgtaacgtca--acttttttttactaaagGAAATCTGGGATGAAGTTGGTGAGAGTGATGATGAACGAGACAAACTGCTTCTTCAGATAGAGCAAGAGTGTCTTGACGTTTACAAGAGAAAAGTCGAGC
upper sequence: GLYMA02G46450.3 (Glycine max), 3'ss of exon 2
lower sequence: AT4G26760.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaactaactacattcagctattcatctttgtcacttaagatgcgaatgctctacagaataatgggattagataattacattatctttatacactgtagGAAATATGGGATGAGGTTGGTGAGAGCGATGAGCAACGAGACAAGATGCTTCTTCAGTTAGAACAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
| || | || || | | || || | |||| | | || | || || | | | | ||||||| |||||||||||||| ||||| ||||| |||||||||| ||||||| ||| | || | ||||| || |||| ||||| | || |||||||
---------------------gtagatttcgcaacatac-acacttatcctttt---aata-tatggttccacaaactcaatgtacaaacttgttacagGAAATCTGGGATGAGGTTGGGGAGAGTGATGAAGAACGAGACAAACTGCTTCTACAGATTGAGGAAGAGTGTCTGAATGTTTACAAAAAGAAAGTTGAGC
upper sequence: GLYMA02G46450.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0090g01230.t01 (Vitis vinifera), 3'ss of exon 1
gtaactaactacattcagctattcatctttgtcacttaagatgcgaatgctctacagaataatgggatta-gataattacatta--tctttatacactgtagGAAATATGGGATGAGGTTGGTGAGAGCGATGAGCAACGAGACAAGATGCTTCTTCAGTTAGAACAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
|| | | ||| || | || || ||| | | || ||| | | | || | ||| | | || | | | | || || |||| ||||||||||||||||| ||||||||| |||| || || ||||| ||||||||||| || ||||||||||| || || ||||| |||||||| |
gtcattgtttacttt--gtgatatattagtgttataagtagaccttgcatactgaggaacagggcaaatacgctaaatgctgtaaaccatggtttaatgcagCAAATCTGGGATGAGGTTGGTGAAAGCGATGAGGAACGTGATAAAATGCTCCTTCAGTTAGAGCAAGAGTGCTTGGACGTTTATAAGAGGAAGGTTGATCMapped 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|17022059|gb|BM093093.1|BM093093EST: ATCCTCTTCTTGGAGAAAACACATGTGGTTCCTTGTTAAAAAAGCTTCAG GAAATATGGGATGAGGTTGGTGAGAGCGATGAGCAACGAGACAAGATGCTT
genomic: ATCCTCTTCTTGGAGAAAACACATGTGGTTCCTTGTTAAAAAAGCTTCAGgtaactaact ... tacactgtagGAAATATGGGATGAGGTTGGTGAGAGCGATGAGCAACGAGACAAGATGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatgctctacagaataatgggattagataattacattatctttatacactgtagGAAATATGGGATGAGGTTGGTGAGAGCGATGAGCAACGAGACAAGATGCTTCTTCAGTTAGAACAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
tctttat CT-rich tract
attagataattacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactaactacattcagctattcatctttgtcacttaagatgcgaatgctctacagaataatgggattagataattacattatctttatacactgtagGAAATATGGGATGAGGTTGGTGAGAGCGATGAGCAACGAGACAAGATGCTTCTTCAGTTAGAACAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA