Sequence
atgc intronic sequence ATGC exonic sequence...cctattgatatctttagctttgattcgtaatagtgtcctattggtgatttatacttaacttggcattgtgcttacttttcccttgtcacttgatttgcagTTTTGCAGCTTTGTTATAATCAGTTGACAGGAAGCATTCCTACACAGCTTGGTGCTTTGGAAAAGCTGAGAGTTGTTGCTTTGCAGTCAAACAATTTAAC
Basic information
species | Glycine max |
transcript | GLYMA20G35520.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35520.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g04370.1 (Oryza sativa), 3'ss of exon 1
----cctattgatatctttagctttgattcgtaatagtgtcctattggtgatttatacttaacttggcattgtgcttacttttcccttgtcacttgatttgcagTTTTGCAGCTTTGTTATAATCAGTTGACAGGAAGCATTCCTACACAGCTTGGTGCTTTGGAAAAGCTGAGAGTTGTTGCTTTGCAGTCAAACAATTTAAC
|| ||| || || || || | || || | |||| | | | || | || || | || || || |||||||||||||||| |||| |||||||||||||| ||||| || | ||| | || | | ||||| ||| |||| | ||||| ||| | | ||
taatatgatacatagacttcgcaatggctcattg-agaatcaaaagtatgatatgatgtggtgcagattttttatgtagcatttctttctctttt---ttgcagTTTTGCAGCTGGGTTACAATCAGTTGACAGGCAGCATACCACCCCAGTTAGGCAAGCTCAACAAGCTTGCTGTTCTTGCACTTCAGTCCAACCAGCTGAC
upper sequence: GLYMA20G35520.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G097313_T01 (Zea mays), 3'ss of exon 1
--cctattgatatct--ttagctttgattcgtaatagtgtcctattggtgatttatacttaacttggcattgtgcttacttttcccttgtcacttgatttgcagTTTTGCAGCTTTGTTATAATCAGTTGACAGGAAGCATTCCTACACAGCTTGGTGCTTTGGAAAAGCTGAGAGTTGTTGCTTTGCAGTC-AAACAATTTAAC
| | | || | || || | | ||| | | || |||||| | | | | | | | ||| || || |||||||| ||||||||| |||| |||||||||||||| ||||| ||| | ||||| || || | ||||| | || | || ||||||| || || || |
gttcagaaaagagctgatgagtttggtcttttaacatcaaa--agtgctgatttgcaat-gccataaattaatttacatagttctctcactaccct-tttgcagTGTTGCAGCTTGGTTACAATCAGTTGACAGGCAGCATACCTCCCCAGCTGGGCAACCTGAATAAGCTAACCGTGCTCGCGATGCAGTCTAATCAGCTTGA-
upper sequence: GLYMA20G35520.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0022g01620.t01 (Vitis vinifera), 3'ss of exon 1
cctattgatatctttagctttgattcgtaat-----agtgtcctattggtgatttatacttaacttggcattgtgcttacttttcccttgtcacttgatttgcagTTTTGCAGCTTTGTTATAATCAGTTGACAGGAAGCATTCCTACACAGCTTGGTGCTTTGGAAAAGCTGAGAGTTGTTGCTTTGCAGTCAAACAATTTAAC
| | ||||| ||| | | | || | | || ||| | || | | | || ||| | | | | | ||| | ||| ||| |||| ||||||| |||||||| ||||| ||||||||||| || |||||||| || ||||| | ||||| || ||| ||||| | || || || | | ||
-aactcagtccatttaggtttcaatagaaagcttcaaacttgcttttgtttatggtttttgatctaaacatca---tcagtatgcttttgcc-tttgtcttgtagTTCTGCAGCTATGTTATAACCAGTTAACAGGAAGCATACCCACACAGCTGGGGTCTTTGAAGAAGCTTAGTGTTCTTGCTCTTCAATCTAATCAGCTTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttatacttaacttggcattgtgcttacttttcccttgtcacttgatttgcagTTTTGCAGCTTTGTTATAATCAGTTGACAGGAAGCATTCCTACACAGCTTGGTGCTTTGGAAAAGCTGAGAGTTGTTGCTTTGCAGTCAAACAATTTAAC
cttacttttcccttgt CT-rich tract
atacttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctattgatatctttagctttgattcgtaatagtgtcctattggtgatttatacttaacttggcattgtgcttacttttcccttgtcacttgatttgcagTTTTGCAGCTTTGTTATAATCAGTTGACAGGAAGCATTCCTACACAGCTTGGTGCTTTGGAAAAGCTGAGAGTTGTTGCTTTGCAGTCAAACAATTTAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
cctattg