Sequence
atgc intronic sequence ATGC exonic sequencegtaactaacttcattcagcttttcatctgtgtcactcaagatgcgaatgctctacagaataatgggataaattaatttcattttctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
Basic information
species | Glycine max |
transcript | GLYMA14G02200.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------gtaactaacttcattcagcttttcat-ctgtgtcactcaagatgcgaatgctctacagaataatgggataaattaatt---tcattttctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
| || | || | | || | | | | || | |||| | || || || ||| | | | || || | || |||||||||||||||||||| ||||| || | || ||||||||| | |||||| |||| || || ||||||||||| |||| |||||||||||| |
gtgcctttgtctcttccaatgttcttttgtatgtgtgctttataatgactggaactaaggatagcagcaagccattttagttccctatctacaccatagcatctgtgcaacgaaaagttatatgagtagtgcataggattggacaagtgactgactagtgtcatttcagTTGATATGGGATGAGGTTGGTGAAAGCGATGAAGACCGTGACAAGATGTTACTTCAGCTAGAACAAGAATGCTTGGATGTTTACAGGAGAAAGGTTGATC
upper sequence: GLYMA14G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g20370.1 (Oryza sativa), 3'ss of exon 2
----gtaactaacttc---attcagctttt--catctgtgtc-actcaagatgcgaatgctctacagaataatgggataaattaatttcattttctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
|| | | | || || |||||| ||| | ||| | | | ||| | | | || |||| | | | ||| ||| || ||||||||||| |||||||||||||||||| | || |||||| | || |||||||| ||||||||| ||||||| |||||||| || ||||| |
gtgcgtgattgatttgttgcttgtgcttttgcgatccgcgtctagtttatgcatttgtgccttgctttgtgttgtgatagtggtgtgcttctgttcttaaa-actgcagTTGATATGGGATGAAGTTGGTGAGAGCGACGAGGACCGCGACAAGGTCCTGTACCAGTTAGATCAGGAGTGCCTGGATGTTTACAAGAGGAAAGTTGACC
upper sequence: GLYMA14G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G112337_T02 (Zea mays), 3'ss of exon 4
gtaactaacttcattcagcttttcatctgtgtcactcaagatgcgaatgctctacagaataatgggataa-attaatttcat---tttctttat-tcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
||| | | | || | | | | | | ||||| | | || | || | | | ||| ||| | | || || | | | | || ||||||||||||||||| || || || || | || ||||||||| | |||||| ||||||| |||||||| ||||| || | |||||||||||| |
--aaccattctaacccattatctagattaag--agttaagatagcatttctacaagaaagagtagtataggattcacacaagtgattgctatgtgttatttcagCTGATATGGGATGAGGTTGGCGAAAGTGATGAAGATCGTGACAAGATGTTACTTCAGCTAGAGCAAGAGTGCTTAGATGTTTATAGGAGAAAGGTTGATC
upper sequence: GLYMA14G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaactaacttcattcagcttttcatctgtgtcactcaagatgcgaatgctctacagaataatgggataaattaatttcattttctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
| | ||| | | ||| ||| | | ||| ||| | | ||| ||| || || || || ||||||| |||||||| ||||||||||| || || |||||||||| ||||||||||| ||||||| ||||| | || || ||||||||||| || ||||
------------gtaaatcttgctaccatctccacctaag-tattagggctttac----tctcaatcttgtgtaacgtcaacttttt--tttactaaagGAAATCTGGGATGAAGTTGGTGAGAGTGATGATGAACGAGACAAACTGCTTCTTCAGATAGAGCAAGAGTGTCTTGACGTTTACAAGAGAAAAGTCGAGC
upper sequence: GLYMA14G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0090g01230.t01 (Vitis vinifera), 3'ss of exon 1
gtaactaacttcattcagcttttcatctgtgtcactcaagatgcgaatgctctacagaataatg-ggataaattaatttcattt--tctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
|| | | || | | | | || |||| | | || ||| | | ||| ||| | | | | | || || || |||| ||||||||||||||||| ||||| ||| |||| || || ||||| |||||||||||||| ||||||||||| || || ||||| |||||||| |
gtcattg--tttactttgtgatatattagtgttataagtagaccttgcatactgaggaacagggcaaatacgctaaatgctgtaaaccatggtttaatgcagCAAATCTGGGATGAGGTTGGTGAAAGCGATGAGGAACGTGATAAAATGCTCCTTCAGTTAGAGCAAGAGTGCTTGGACGTTTATAAGAGGAAGGTTGATC
upper sequence: GLYMA14G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S11_105V6.1 (Physcomitrella patens), 3'ss of exon 1
-gtaactaacttcattcagcttttcatctgtgtcactcaagatgcgaatgctctacagaataatgggataaattaatttcattttctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
| || | ||| | ||| || | | ||| || | | | | | | | | | ||| || || | ||||||||||| ||||| || ||||||| || |||| ||||||||| | |||||||||||||| || | || || |||| | || || ||
gtcagcttgtgttattagg--tttgattcaagcctgatttattgcatttgatattattcacttcgttctggacgtttgctgatatggagattgattgcagCACATATGGGATGAAGTTGGAGAAAGCGACGCCGAAAGAGATAAGATGCTTTTACAGTTAGAGCAGGAATGTCTAGAGGTTTACAGACGGAAAGTGGATAMapped 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|298165214|gb|HO011263.1|HO011263EST: ATCCTCTTCTTGGAGAAAACACATGTGGTTCCTTGTTAAAAAAGCTTCAG GAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTT
genomic: ATCCTCTTCTTGGAGAAAACACATGTGGTTCCTTGTTAAAAAAGTTTCAGgtaactaact ... ttcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTT
EST:
gi|7232523|gb|AW567878.1|AW567878EST: ATCCTCTTCTTGGAGAAAACACATGTGGTTCCTTGTTAAAAAAGCTTCAG GAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTT
genomic: ATCCTCTTCTTGGAGAAAACACATGTGGTTCCTTGTTAAAAAAGTTTCAGgtaactaact ... ttcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatgctctacagaataatgggataaattaatttcattttctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
aattaat putative branch site (score: 3)
tttcattttctttatt CT-rich tract
aataatgggataaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactaacttcattcagcttttcatctgtgtcactcaagatgcgaatgctctacagaataatgggataaattaatttcattttctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA