Sequence
atgc intronic sequence ATGC exonic sequence...gtttgatgtgtagattatcaataatgcacaaatatcttcgttagcatttatcttgcaaagtggactgactgcttggttatcaataatttatccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAATGATGTGTACCTTGTTTCTGAGTTAATGGACACAGATCTGCATCAAATAA
Basic information
species | Glycine max |
transcript | GLYMA16G03670.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
-------gtttgatgtgtagattatcaataatgcacaa-atatcttcg--tta-gcatttatcttgcaaagtggactgactgcttggttatcaataatttatccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAATGATGTGTACCTTGTTTCTGAGTTAATGGACACAGATCTGCATCAAATAA
||| ||| | | |||| | | | | || || | | | ||||||| | | ||| |||| | || || | || | | ||| |||||||| |||| || || || || || || ||| | || ||||| |||||||| ||| ||||||||||||| ||||| || ||||| ||||| || |
ttccttttttttttgt-tgggcggtcaagagcgtgtgatacatttttgactcacacatttatatcatatagt---ctgatgg--tgatt-ttaacactggatc----acagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
upper sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 2
gtttg-atgtgt--agattatcaataatgcacaaatatcttcgttagcatttatcttgcaaagtggactgact-gcttggttatcaa--taatttatccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAATGATGTGTACCTTGTTTCTGAGTTAATGGACACAGATCTGCATCAAATAA
| || |||||| | ||||| ||| | ||| | | |||| | | || | | || || | | | | | || | ||| || | ||||| | || | || ||| | || || || ||| | || ||||| ||||| |||||| ||||| ||||||||||||| |||||||| ||||| ||
-tatgcatgtgttagaaccatcaaccatgt-tgtacttctac-tcagcaatgaagttccta--tgatctaatttgtctaataatgattttaacttgtg-gtcacagATCCTTGCCTTAAAGGATGTAATTCGGCCCCCAACTAGAGAGAACTTTAATGACGTGTACATTGTTACTGAGTTAATGGATACAGATCTCCATCAGATCG
upper sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 2
gtttgatg--tgtagattatcaataatgcacaaatatcttcgttagcatttatcttgcaaagtggactgactgcttggttatcaataatttatccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAATGATGTGTACCTTGTTTCTGAGTTAATGGACACAGATCTGCATCAAATAA
||| | | | | | | | || | ||| | | | | | ||||| | | || ||||| | |||||| |||| |||| | | ||||| || ||||| || || ||| ||| |||||||||||||| ||| |||||| ||| ||||||||||| ||||||||||| ||||
ctttagttactttggttcgtttgttggattcaggt-tctagaattttttatgttcctcctggtggaataatatatttactatcagtt-cttatcctccgcagGTTATTGTCTTGAAAGACATCATACGGCCACCTAAGAGGGAGAACTTCAATGATGTCTACATTGTTTATGAATTAATGGACACTGATCTGCATCAGATAAMapped 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|23052819|gb|BU577310.1|BU577310EST: AAAGGACCTTACGGGAAATTAAACTTCTTCGGCACATGGATCATGCAAAT ATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
genomic: AAAGGACCTTACGGGAAATTAAACTTCTTCGGCACATGGATCATGCAAATgtaagtttga ... tccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttatcttgcaaagtggactgactgcttggttatcaataatttatccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAATGATGTGTACCTTGTTTCTGAGTTAATGGACACAGATCTGCATCAAATAA
gactgac putative branch site (score: 2)
tttatcc putative PPT
ttatcaataatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgatgtgtagattatcaataatgcacaaatatcttcgttagcatttatcttgcaaagtggactgactgcttggttatcaataatttatccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAATGATGTGTACCTTGTTTCTGAGTTAATGGACACAGATCTGCATCAAATAA
- -tgatgtg
- - - - - - - - - - - aatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgactgc