Sequence
atgc intronic sequence ATGC exonic sequence...taacgctgttacaaaggaaacatggttgacattcttgttatgttactttcaaggaaatacgtaaaatttggttctgttgttaacaaagacttgtgtacagGTATGTGGTGAAGACATTGGACAATGCAGAGAGTGTAAAGTTGCAGTATCGATCCCTTGCCAAGGTTATGGATGATCCTTCAAAACCTGCAGCCTCCAGC
Basic information
species | Glycine max |
transcript | GLYMA04G40060.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G40060.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g60140.1 (Oryza sativa), 3'ss of exon 7
taacgctgttacaaaggaaacatggttgacattcttgttatgttactttcaa---ggaaatacgtaaaatttggttctgttgttaacaaagacttgtgtac-agGTATGTGGTGAAGACATTGGACAATGCAGAGAGTGTAAAGTTGCAGTATCGATCCCTTGCCAAGGTTATGGATGATCCTTCAAAACCTGCAGCCTCCAGC
| | || | || || | ||| || | || | | || | || ||| | || || || ||||||||||||||||| || ||||||||||||||||| |||||||| || || || || || ||| ||| |||| |||| |
-----------------------gttagaaacatttttttcccaagttttaatatgatcatcgttgatatcaaacaccgtgcttacccggtacctgcacaccagGTATGTGGTGAAGACCTTAGACAATGCAGAGAGTGTGAAGTTGCAATACCGTTCTCTGGCTAAGTTTACTGATGGCGGCCAGTCCTCTGCTATGGTCGCA
upper sequence: GLYMA04G40060.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G05230.1 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------------------------------------------taacgctgttacaaaggaaacatggttgacattcttgttatgttactttcaaggaaatacgtaaaatttgg--ttctgttgttaacaaagacttgtgtacagGTATGTGGTGAAGACATTGGACAATGCAGAGAGTGTAAAGTTGCAGTATCGATCCCTTGCCAAGGTTATGGATGATCCTTCAAAACCTGCAGCCTCCAGC
||| | | || ||| | | | || | | || | | | | || || | || ||| || || ||| | ||||||||||||||| ||| ||||||| ||||||||||| ||| | |||||||| || | || || | | || ||||| ||| ||| | | | |
gtaaagtctcatttctttctttgattcactaagtttagattctttctcactgcaaactttaaagacatcaccttaataaccttgagcaaatatctataccaacttttgtataaattttctgtaacttcagagctcatttgctacataaaactatattgcagGTATGTGGTGAAAACACTGGACAACGCAGAGAGTGTGAAGCTTCAGTATCGTTCATTGGCTAAAGCTCCAGAAGATCCATCAGCTAAAGCAACACCAAAC
upper sequence: GLYMA04G40060.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv13s0067g03030.t01 (Vitis vinifera), 3'ss of exon 7
taacgctgttacaaagga-aacatggttgacattcttgttatgttactttcaaggaaat--acgtaaaatttggttctgttgttaa--caaagacttgtgtacagGTATGTGGTGAAGACATTGGACAATGCAGAGAGTGTAAAGTTGCAGTATCGATCCCTTGCCAAGGTTATGGATGATCCTTCAAAACCTGCAGCCTCCAGC
| || || ||||| | | | | | ||| | || | | |||| | | | || || | ||| | | | |||||||||||||||||||||||||| |||||||||||||| || |||||||||| || || ||||||||| ||| |||| || | || | |||
----agtattgcatgccttgacatgat-attaccacaaatttctcactgtgaaaagtaccgatttaaattgccatacatttattcatacaataattcatctacagGTATGTGGTGAAGACATTGGATAATGCAGAGAGTGTTAAACTGCAGTATCGTTCACTCGCCAAGGTTCCAGATAATCCATCCTCAAAGCCAATGTTGAGCMapped 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|21285816|gb|BQ473687.1|BQ473687EST: CGCTTTGTTGGGCGCGAAGCTATTGTTACAACGCAATGCCTGAATGGATG GTATGTGGTGAAGACATTGGACAATGCAGAGAGTGTAAAGTTGCAGTATCG
genomic: CGCTTTGTTGGGCGCGAAGCTATTGTTACAACGCAATGCCTGAATGGATGgttagtgact ... ttgtgtacagGTATGTGGTGAAGACATTGGACAATGCAGAGAGTGTAAAGTTGCAGTATCG
EST:
gi|11688477|gb|BF596153.1|BF596153EST: CGCTTTGTTGGGCGCGAAGCTATTGTTACAACGCAATGCCTGAATGGATG GTATGTGGTGAAGACATTGGACAATGCAGAGAGTGTAAAGTTGCAGTATCG
genomic: CGCTTTGTTGGGCGCGAAGCTATTGTTACAACGCAATGCCTGAATGGATGgttagtgact ... ttgtgtacagGTATGTGGTGAAGACATTGGACAATGCAGAGAGTGTAAAGTTGCAGTATCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttcaaggaaatacgtaaaatttggttctgttgttaacaaagacttgtgtacagGTATGTGGTGAAGACATTGGACAATGCAGAGAGTGTAAAGTTGCAGTATCGATCCCTTGCCAAGGTTATGGATGATCCTTCAAAACCTGCAGCCTCCAGC
tgttaac putative branch site (score: 2)
aaatacgtaaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taacgctgttacaaaggaaacatggttgacattcttgttatgttactttcaaggaaatacgtaaaatttggttctgttgttaacaaagacttgtgtacagGTATGTGGTGAAGACATTGGACAATGCAGAGAGTGTAAAGTTGCAGTATCGATCCCTTGCCAAGGTTATGGATGATCCTTCAAAACCTGCAGCCTCCAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - gctgtta
- - - - - - aaaggaaa
- - - - - - - - - - - - - -gacattc
- - - - - - - - - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gaaatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgttg