Sequence
atgc intronic sequence ATGC exonic sequencegtaactaacttcattcagcttttcatctgtgtcacttaagatgcgaatgctctacagaataatgggataaattaattacattttctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
Basic information
species | Glycine max |
transcript | GLYMA14G02180.4 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G02180.4 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------gtaactaacttcattcagcttttcat-ctgtgtcacttaagatgcgaatgctctacagaataatgggataaattaattac---attttctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
| || | || | | || | | | | || | | |||| | || || || ||| | | | || || | || |||||||||||||||||||| ||||| || | || ||||||||| | |||||| |||| || || ||||||||||| |||| |||||||||||| |
gtgcctttgtctcttccaatgttcttttgtatgtgtgctttataatgactggaactaaggatagcagcaagccattttagttccctatctacaccatagcatctgtgcaacgaaaagttatatgagtagtgcataggattggacaagtgactgactagtgtcatttcagTTGATATGGGATGAGGTTGGTGAAAGCGATGAAGACCGTGACAAGATGTTACTTCAGCTAGAACAAGAATGCTTGGATGTTTACAGGAGAAAGGTTGATC
upper sequence: GLYMA14G02180.4 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g20370.1 (Oryza sativa), 3'ss of exon 2
----gtaactaacttc---attcagctttt--catctgtgtc-acttaagatgcgaatgctctacagaataatgggataaattaattacattttctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
|| | | | || || |||||| ||| | ||| | || | ||| | | | || |||| | | | | | | | ||| || ||||||||||| |||||||||||||||||| | || |||||| | || |||||||| ||||||||| ||||||| |||||||| || ||||| |
gtgcgtgattgatttgttgcttgtgcttttgcgatccgcgtctagtttatgcatttgtgccttgctttgtgttgtgatag-tggtgtgcttctgttcttaaaactgcagTTGATATGGGATGAAGTTGGTGAGAGCGACGAGGACCGCGACAAGGTCCTGTACCAGTTAGATCAGGAGTGCCTGGATGTTTACAAGAGGAAAGTTGACC
upper sequence: GLYMA14G02180.4 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G112337_T02 (Zea mays), 3'ss of exon 4
gtaactaacttcattcagcttttcatctgtgtcacttaagatgcgaatgctctacagaataatgggata--aattaattacattttctttattcgctgt---agGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
||| | | | || | | | | | ||||||| | | || | || | | | ||| | | | | | | ||| | | | || ||||||||||||||||| || || || || | || ||||||||| | |||||| ||||||| |||||||| ||||| || | |||||||||||| |
--aaccattctaacccattatctagattaag--agttaagatagcatttctacaagaaagagtagtataggattcacacaagtgattgctatgtgttatttcagCTGATATGGGATGAGGTTGGCGAAAGTGATGAAGATCGTGACAAGATGTTACTTCAGCTAGAGCAAGAGTGCTTAGATGTTTATAGGAGAAAGGTTGATC
upper sequence: GLYMA14G02180.4 (Glycine max), 3'ss of exon 2
lower sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaactaacttcattcagcttttcatctgtgtcacttaagatgcgaatgctctacagaataatgggataaattaattacattttctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
| | ||| | | ||| |||| | | ||| ||| | | ||| || || || || || ||||||| |||||||| ||||||||||| || || |||||||||| ||||||||||| ||||||| ||||| | || || ||||||||||| || ||||
------------gtaaatcttgctaccatctccacctaag-tattagggctttac----tctcaatcttgtgtaacgtcaacttttt--tttactaaagGAAATCTGGGATGAAGTTGGTGAGAGTGATGATGAACGAGACAAACTGCTTCTTCAGATAGAGCAAGAGTGTCTTGACGTTTACAAGAGAAAAGTCGAGC
upper sequence: GLYMA14G02180.4 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0090g01230.t01 (Vitis vinifera), 3'ss of exon 1
gtaactaacttcattcagcttttcatctgtgtcacttaagatgcgaatgctctacagaataatgggataaattaattacattttct------ttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
|| | | || | | | | || |||| | |||| | ||| ||| || || || |||| || || | | | || || || |||| ||||||||||||||||| ||||| ||| |||| || || ||||| |||||||||||||| ||||||||||| || || ||||| |||||||| |
gtcattg--tttactttgtgatatattagtgtta--taagtagaccttgca-tactgaggaacagggcaaatacgctaaatgctgtaaaccatggtttaatgcagCAAATCTGGGATGAGGTTGGTGAAAGCGATGAGGAACGTGATAAAATGCTCCTTCAGTTAGAGCAAGAGTGCTTGGACGTTTATAAGAGGAAGGTTGATC
upper sequence: GLYMA14G02180.4 (Glycine max), 3'ss of exon 2
lower sequence: PP1S11_105V6.1 (Physcomitrella patens), 3'ss of exon 1
-gtaactaacttcattcagcttttcatctgtgtcacttaagatgcg-aatgctctacagaataatgggataaattaattacattttctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
| || | ||| | || | | | ||| || | | || | | || | | || ||| || || | ||||||||||| ||||| || ||||||| || |||| ||||||||| | |||||||||||||| || | || || |||| | || || ||
gtcagcttgtgttattaggtttgattcaagcctgatttattgcatttgatattattcacttcgttctggacgtttgctgatatgg---agattgattgcagCACATATGGGATGAAGTTGGAGAAAGCGACGCCGAAAGAGATAAGATGCTTTTACAGTTAGAGCAGGAATGTCTAGAGGTTTACAGACGGAAAGTGGATAMapped 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|193542059|gb|FK494519.1|FK494519EST: ATCCTCTTCTTGGAGAAAACACATGTGGTTCTTTGTTAAAAAAGCTTCAG GAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTT
genomic: ATCCTCTTCTTGGAGAAAACACATGTGGTTCCTTGTTAAAAAAGCTTCAGgtaactaact ... ttcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatgctctacagaataatgggataaattaattacattttctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
aattaat putative branch site (score: 3)
ttttctttattcgct putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactaacttcattcagcttttcatctgtgtcacttaagatgcgaatgctctacagaataatgggataaattaattacattttctttattcgctgtagGAAATATGGGATGAGGTTGGTGAGAGCGACGAGCAACGAGACAAGATGCTTCTTCAGTTAGAGCAGGAGTGCTTGGATGTGTACAAGAGAAAGGTTGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA