Sequence
atgc intronic sequence ATGC exonic sequence...ttattcctgatttatctgtgatgctgactgattaactgtgatgcattaaacgcaattgttttccactttcatctcataactgttgattgtgtttgatcagGATGGAGTCTCAGGTGAAGCATGCTCTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAGGTGACTCAGGTTAGAGTGAAGTTTTTGGATGAT
Basic information
species | Glycine max |
transcript | GLYMA03G36420.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G36420.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G455828_T01 (Zea mays), 3'ss of exon 1
ttattcctgatttatc-tgtgatgctgactgattaactgtg--atgcattaaacgcaattgttttccactttcatctcataactgttgattgtgtttgatcagGATGGAGTCTCAGGTGAAGCATGCTCTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAGGTGACTCAGGTTAGAGTGAAGTTTTTGGATGAT
| | | | | ||||| || | | | || || ||| | || ||| || || | | || | || || | || | || ||| ||||| | |||||||||| |||| |||| || || || ||||| | || || ||||| || |||||||| ||||| ||||||||||||||||||||
ccagtagcaacaaaccatgtgacagtg-cagttaaaatgaactatgtgatcaaagcatatggttcaccttgattactgacaaatgct--ttctattaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC
upper sequence: GLYMA03G36420.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G10090.1 (Arabidopsis thaliana), 3'ss of exon 1
---ttattcctgatttatctgtgatgctgactgattaactgtgatgcattaaacgcaattgttttccactttcatctcataac-tgttgattgtgtttgatcagGATGGAGTCTCAGGTGAAGCATGCTCTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAGGTGACTCAGGTTAGAGTGAAGTTTTTGGATGAT
| || ||||| | ||||| | | | | | | | || | | | || | | ||| |||| || | || || |||| ||||| ||||| |||||| | ||||| ||| |||| || ||||| ||||| | |||||||| || || || ||||||||||||||||||||||| ||
tatacagtcttgattcaaatgtga--acaattctctttttctaaggatttt--cacttcttttgtaaaatttggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG
upper sequence: GLYMA03G36420.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
-------ttattcctgatttatctgtgatgctga-ctgattaactgtgatgcattaaacgcaattgttttccactttcatctcataactgttgattgtgtttgatcagGATGGAGTCTCAGGTGAAGCATGCTCTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAGGTGACTCAGGTTAGAGTGAAGTTTTTGGATGAT
|| | | | || | | | | ||||| ||| || | | | ||| | || | | || | | | | | | ||||| | ||||||||||||| | || || |||||||||||||| |||||||| || || |||||||| ||||| ||||||||||||||||
aatgagtttgcttttatagaacttgaaaggaaaaaccaattaa--atgaaaaatggtgcttagt-atttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----
upper sequence: GLYMA03G36420.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 4
-----ttattcctgattta-tctgtgatgctgactgattaactgtgatgcattaaacgcaattgttttccactttcatctcataactgttgattgtgtttgat-cagGATGGAGTCTCAGGTGAAGCATGCTCTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAGGTGACTCAGGTTAGAGTGAAGTTTTTGGATGAT
||||| | | || ||| || || | || | || |||| | || | || | || | | ||| |||| | | || ||||| ||| ||||||||||||| | || || |||||||||||||| ||||| || ||||| |||||||| ||||| || |||||||||||||
tatacatattctttaaatagtctatgtaactaga-aagaaaatacaatcttttaattgatgcccttatgcatctattataaatgatt-ttgtttgtttgcagTGCAAAATGGAATCTGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGCTCAAGAGGTCAGGTGACCCAGGTGAGGGTGAAGTTTTTGG-----Mapped 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|14259739|gb|BG882647.1|BG882647EST: ATCCACCGCTGGCTGATCCTTCTTCTCTAACTCTAATTTATTATTTTCAT GATGGAGTCTCAGGTGAAGCATGCTCTTGTTGTCAAAGTTATGGGTCGTAC
genomic: ATCCACCGCTGGCTGATCCTTCTTCTCTAACTCTAATTTATTATTTTCATgtattgttct ... gtttgatcagGATGGAGTCTCAGGTGAAGCATGCTCTTGTTGTCAAAGTTATGGGTCGTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaacgcaattgttttccactttcatctcataactgttgattgtgtttgatcagGATGGAGTCTCAGGTGAAGCATGCTCTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAGGTGACTCAGGTTAGAGTGAAGTTTTTGGATGAT
aattgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttattcctgatttatctgtgatgctgactgattaactgtgatgcattaaacgcaattgttttccactttcatctcataactgttgattgtgtttgatcagGATGGAGTCTCAGGTGAAGCATGCTCTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAGGTGACTCAGGTTAGAGTGAAGTTTTTGGATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - -cctgatt
- - - - - - -atctgtg
- - - - - - - - - - -tgctgac
- - - - - - - - - - - - - - - - -aactgtg
- - - - - - - - - - - - - - - - - - - - -tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgttg