Sequence
atgc intronic sequence ATGC exonic sequence...actgatcttgttcatgttttaatctttaagtttgtttgaacatacttcctgttgttttatgcttcatagaatcttacgcaaaatatttgtttgactccagGAGTGGGTTTTGGCCCTGGAATTCCTGGTTTCCAAGTTGGTTTTGGATTTGGAGCTGGATGTGGAGTTGGTTTTGGGTTTGGCTATGGTGTGGGGAAAGG
Basic information
species | Glycine max |
transcript | GLYMA16G33040.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G33040.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g13880.1 (Oryza sativa), 3'ss of exon 1
actgatcttgttcatgttttaatct----ttaagtttgtttgaacat-acttcctgttgttttatgcttcataga--atcttacgcaaaatatttgtttgact--ccagGAGTGGGTTTTGGCCCTGGAATTCCTGGTTTCCAAGTTGGTTTTGGATTTGGAGCTGGATGTGGAGTTGGTTTTGGGTTTGGCTATGGTGTGGGGAAAGG
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---------ggtgatattttaaactcacattatgtccatgtaaccatgacaattcaatccctttttttccatggatggtgtataatcatttctttttatgaatgtttagGTGCAGGATTAGGTTATGGATTTCCCGGACTCACATTAGGCTTTGGAGTTGGAGCTGGATGTGGTGTAGGATTTGGCTTTGGTTATGGATTGGGGAAAGG
upper sequence: GLYMA16G33040.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G10330.1 (Arabidopsis thaliana), 3'ss of exon 1
-------actgatcttgttcatgttttaatctttaagt------ttgtttgaacatacttcctgttgttttatgcttcatagaatcttacgcaaaatatttgtttgactccagGAGTGGGTTTTGGCCCTGGAATTCCTGGTTTCCAAGTTGGTTTTGGATTTGGAGCTGGATGTGGAGTTGGTTTTGGGTTTGGCTATGGTGTGGGGAAAGG
|| || | || |||| ||| | | | | | ||| || || | | ||| | || | ||| | | | | || ||| |||| || || || || || ||| ||||||| || ||| ||||| |||||||||||||||| |||||| ||||| | || |||||||||||||| || | |||
gtaaatttctaatttctccca-attttgatcgcagactcgcgaatcgctcgaagctatttatagatagttttggtttaagagagt-----agagattggtttgatgaaaacagGTGTAGGATTCGGACCAGGAGTTCCTGGATTACAATTTGGTCTTGGATTTGGAGCTGGTTGTGGAATTGGTGTAGGTTTTGGCTATGGTGTTGGAAGAGG
upper sequence: GLYMA16G33040.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0089g01180.t01 (Vitis vinifera), 3'ss of exon 1
actgatcttgttcatgttttaatctttaagtttgtttgaacatacttcctgttgttttatgcttcatagaatctt--acgcaaaatatttgtttgactccagGAGTGGGTTTTGGCCCTGGAATTCCTGGTTTCCAAGTTGGTTTTGGATTTGGAGCTGGATGTGGAGTTGGTTTTGGGTTTGGCTATGGTGTGGGGAAAGG
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-ataatgctccttaccccttgatcct-aattcaaaatgatgtttaatgaaaaattcttctgcttagtggaagtgtgaatgcttaaacaattttttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTGGTGCTGGATGTGGGGTTGGTTTAGGATTTGGTTATGGTGTGGGGAGGGGMapped 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|298189064|gb|HO037467.1|HO037467EST: CGGCATCGGCGCCGGCTGCGGCCTCGGTTTCGGCCTTGGCCTTCTCGGAG GAGTGGGTTTTGGCCCTGGAATTCCTGGTTTCCAAGTTGGTTTTGGATTTG
genomic: CGGCATCGGCGCCGGCTGCGGCCTCGGTTTCGGCCTTGGCCTTCTCGGAGgttcattctt ... ttgactccagGAGTGGGTTTTGGCCCTGGAATTCCTGGTTTCCAAGTTGGTTTTGGATTTG
EST:
gi|10235780|gb|BE804668.1|BE804668EST: CGGCATCGGCGCCGGCTGCGGCCTCGGTTTCGGCCTTGGCCTTCTCGGAG GAGTGGGTTATGGCCCTGGAATTCCTGGTTT
genomic: CGGCATCGGCGCCGGCTGCGGCCTCGGTTTCGGCCTTGGCCTTCTCGGAGgttcattctt ... ttgactccagGAGTGGGTTTTGGCCCTGGAATTCCTGGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcctgttgttttatgcttcatagaatcttacgcaaaatatttgtttgactccagGAGTGGGTTTTGGCCCTGGAATTCCTGGTTTCCAAGTTGGTTTTGGATTTGGAGCTGGATGTGGAGTTGGTTTTGGGTTTGGCTATGGTGTGGGGAAAGG
tttgttt CT-rich tract
aaaatatttgtttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgatcttgttcatgttttaatctttaagtttgtttgaacatacttcctgttgttttatgcttcatagaatcttacgcaaaatatttgtttgactccagGAGTGGGTTTTGGCCCTGGAATTCCTGGTTTCCAAGTTGGTTTTGGATTTGGAGCTGGATGTGGAGTTGGTTTTGGGTTTGGCTATGGTGTGGGGAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - -tcatgtt
- - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttca