Sequence
atgc intronic sequence ATGC exonic sequence...agaatttggccagattctaatcttgtgattgctttcttagatgtactatcattgtggatccttttgtgcttaaattattaaattaacttgtctatgacagGGAGCTCTACAGTAATAACATAAGTGGACCAATTCCTAGTGACCTTGGGAATCTAACTAGCTTGGTGAGCTTGGATCTTTATTTGAACAGTTTTACTGGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os08g07760.1 (Oryza sativa), 3'ss of exon 3
agaatttggccagattctaatcttgtgattgctttcttagatgtactatcattgtggatccttttgtgcttaaattattaaattaacttgtctatga--cagGGAGCTCTACAGTAATAACATAAGTGGACCAATTCCTAGTGACCTTGGGAATCTAACTAGCTTGGTGAGCTTGGATCTTTATTTGAACAGTTTTACTGGT
|||| | || | | ||||| | | | | | |||| || | || | || | | || | || ||| | ||||| ||||||||||||||||||||||||||| ||| | || |||||||| ||||| || || || | |||||| || |||||| | || ||||||| || ||||||
agaaatattcctagctagtgtgttgtgctcagatcaactcaagc-caatcactgagtattgtagagtattaatgttcattgtttt-cttctttatgatgcagGGAGCTCTACAGTAATAACATAAGCGGAACGATACCTAGTGAACTTGGAAACCTCACAAACTTGGTCAGTTTGGATTTGTACTTGAACAACTTCACTGGT
upper sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g38480.1 (Oryza sativa), 3'ss of exon 3
agaatttggccagattctaatcttgtgattgctttcttagatgtactatcattgtggatccttttgtgcttaaattattaaattaacttgt---ctatgacagGGAGCTCTACAGTAATAACATAAGTGGACCAATTCCTAGTGACCTTGGGAATCTAACTAGCTTGGTGAGCTTGGATCTTTATTTGAACAGTTTTACTGGT
|| | | || |||||| | | | | | | | | | | | | ||| | | | ||| ||||| |||| || |||||||||| ||||| || ||||||||||| |||| |||| ||| || || || |||||| |||||| || ||||||||||| |||||| || ||||||
--tcttggaatatggcttatccttgtggtaaagatggttgtgttgccaccttctttcttgcatttttattgtgaa-atttaattatgttgtgactaattacagGGAGCTTTACAGCAACAACATAAGTGGGACAATACCTAATGAACTGGGAAACTTAACTAACTTGGTCAGTTTGGATCTTTACCTGAACAACTTCACTGGT
upper sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G384439_T02 (Zea mays), 3'ss of exon 3
agaatttggccagattctaatcttgtgattgctttcttagatgtactatcattg---tggatccttttgtgcttaaa-ttattaaat-------taacttgtctatg-acagGGAGCTCTACAGTAATAACATAAGTGGACCAATTCCTAGTGACCTTGGGAATCTAACTAGCTTGGTGAGCTTGGATCTTTATTTGAACAGTTTTACTGGT
| | | || | || || | | | || | | | ||||||| ||||| ||| | | | || | ||| | | |||||||||||||||||||||| || ||||| | || |||||||| ||||||||||| || | |||||| || |||||| | || ||||||| || ||||||
----------tcactaatgacctca--accatttactgtggcatgccatagcttggttactttcttttgtttttaaaattagtcactgccttcatatcgtgtttttatacagGGAGCTCTACAGTAATAATATCAGTGGCACTATACCTAGTGAACTTGGGAATCTTACAAACTTGGTCAGTTTGGATTTGTACTTGAACAACTTCACTGGT
upper sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G31320.1 (Glycine max), 3'ss of exon 3
-agaatttggccagattctaatcttgtgattgctttcttag-atgtact--atcattgtggatccttttgtgcttaaattattaaattaacttgtctatgacagGGAGCTCTACAGTAATAACATAAGTGGACCAATTCCTAGTGACCTTGGGAATCTAACTAGCTTGGTGAGCTTGGATCTTTATTTGAACAGTTTTACTGGT
| |||| | | || | | |||| ||| || || | | | || | || |||| | | || | ||| || || | ||||| |||||||| |||||||| | ||| || ||||| |||||||| |||||||| |||| |||||||||||||||||| || | || ||| |||||
aacaatt--gtaaagtttttggcagatgatgattttaataatattgatttaaatatctttagtctttttatatctttttttgtttattgttttac--ataatagGGAACTCTACAGCAATAACATTACTGGCCCTATTCCAAGTGACCTGGGGAATCTTACTAACTTGGTGAGCTTGGATCTGTACCTAAATCATTTCACTGGC
upper sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G08360.1 (Glycine max), 3'ss of exon 2
agaatttggccagattctaatcttgtgattgctttcttagatgtactatcattgtggat-ccttttgtgcttaaattatta---aattaacttgtctatgacagGGAGCTCTACAGTAATAACATAAGTGGACCAATTCCTAGTGACCTTGGGAATCTAACTAGCTTGGTGAGCTTGGATCTTTATTTGAACAGTTTTACTGGT
|| || || || || | | | |||| || | | ||| | | ||||| || | | | | ||| ||| |||| | || || || | || || || ||||| |||||||| |||||||||||||| | |||||| |||||||| |||| ||||||||||||||||| ||| | ||| |||| | |||
agccttgaaacaaat-ctggtagc-taaatgctaatttt-acaaaatattaatttggatatctgatatcttcatatttttatgtaatttatttttc-ataatagAGAACTTTACAGCAATAACATTAGTGGACCAATTCCAAATGACCTGGGGAATCTTACTAATTTGGTGAGCTTGGATCTGTATCTAAACCGTTTCAGTGGA
upper sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G36280.1 (Glycine max), 3'ss of exon 3
-----------agaatttggccagattctaatcttgtgattgctttcttagatgtactatcattgtggatccttttgtgcttaaattattaaattaacttgtctatgacagGGAGCTCTACAGTAATAACATAAGTGGACCAATTCCTAGTGACCTTGGGAATCTAACTAGCTTGGTGAGCTTGGATCTTTATTTGAACAGTTTTACTGGT
| ||||| | |||| || || || | | | ||| || | | | | ||| ||||| || ||| || ||| || | ||||| || ||||| |||||||| | ||| || ||||| |||||||| |||||||| |||| |||||||||||||||||| || ||||| ||| |||||
gaaatattataaaaatttaggcagaagctgattttactaatattgatttaaatatctttaatctttatatctttttg-atgtatattgtt---tta-------cataatagGGAACTTTACAGCAATAACATTACTGGCCCTATTCCAAGTGACCTGGGGAATCTTACTAACTTGGTGAGCTTGGATCTGTACCTGAACCATTTCACTGGCMapped 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|71873068|gb|DT022123.1|DT022123EST: TCGGGTCAACTGGTACCACAGCTTGGCCTCCTTAAGAATTTGCAGTACTT GGAGCTCTACAGTAATAACATAAGTGGACCAATTCCTAGTGACCTTGGGAA
genomic: TCGGGTCAACTGGTACCACAGCTTGGCCTCCTTAAGAATTTGCAGTACTTgtaagctatg ... tctatgacagGGAGCTCTACAGTAATAACATAAGTGGACCAATTCCTAGTGACCTTGGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatcattgtggatccttttgtgcttaaattattaaattaacttgtctatgacagGGAGCTCTACAGTAATAACATAAGTGGACCAATTCCTAGTGACCTTGGGAATCTAACTAGCTTGGTGAGCTTGGATCTTTATTTGAACAGTTTTACTGGT
aattaac putative branch site (score: 2)
cttgtct CT-rich tract
ttttgtgcttaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaatttggccagattctaatcttgtgattgctttcttagatgtactatcattgtggatccttttgtgcttaaattattaaattaacttgtctatgacagGGAGCTCTACAGTAATAACATAAGTGGACCAATTCCTAGTGACCTTGGGAATCTAACTAGCTTGGTGAGCTTGGATCTTTATTTGAACAGTTTTACTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - -tgattgc
- - - - - - - - - - - - - - - - - - - - - - - - - -ttgtgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaattaa