Sequence
atgc intronic sequence ATGC exonic sequencegtctgatgtactgttttttttatatatatatatttttaaatattaatataatccttttgatgaggatgcagttgctcaaaatgtgtgcttgtgcagTTCACAGACGAAAATGGGTTAAGGGAATATGTTTGGCAGACATCATGGGCAATTAGTACACGTTTTGTTGGTGGCATCATCATGACACATGGAGATGATG
Basic information
species | Glycine max |
transcript | GLYMA09G24670.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G24670.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g07060.1 (Oryza sativa), 3'ss of exon 4
-------gtctgatgtactgttttttttatatatatatatttttaaatattaatataatccttttgatgaggatgcagttgctcaaaatgtgtgcttgtgcagTTCACAGACGAAAATGGGTTAAGGGAATATGTTTGGCAGACATCATGGGCAATTAGTACACGTTTTGTTGGTGGCATCATCATGACACATGGAGATGATG
|||| | ||| | | | ||| | || || || | || | |||| || |||| || | ||| || ||||| | || |||||| | || ||| ||||||||||||| || ||||| ||||| || || ||||||||||| ||||||||||| ||||| |||||||
tccagagacttgatttggtgtctcacctgcgt-tatttcttgtttgcattttctttagctacatccatgatcttgaagttcttctcttcctttgcctg--cagTTTATGGATGAAAATAGCCAAATCGAACATGTTTGGCAGACTTCTTGGGCTATTAGCACTCGGTTTGTTGGTGGGATCATCATGACCCATGGTGATGATG
upper sequence: GLYMA09G24670.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G107089_T01 (Zea mays), 3'ss of exon 6
------------------------------------------------gtctgatgtactgttttttttatatatatatatttttaaatatt--aatataatccttttgatga------ggatgcagttgctcaaaatgtgtgc-ttgt--gcagTTCACAGACGAAAATGGGTTAAGGGAATATGTTTGGCAGACATCATGGGCAATTAGTACACGTTTTGTTGGTGGCATCATCATGACACATGGAGATGATG
| || | | | ||| | || | || || ||| | | | || |||| || | | || | | | | | | |||| |||||| | || |||||||| || ||| | || |||||||| || ||||| |||||||| || ||||||||||| || |||||||| ||||| |||||||
gttgctaccaactctcttcatatcgtgatgacttcatgtgttggatccattctatacattttaaaatttcagaacattttttcacaaggattggattttgttctttttaattctttcttgttttcaaacattttgatttttttcattgtctgcagTTTATGGATGAAAATGGTCAAATCGAACACGTCTGGCAGACCTCTTGGGCTATTAGTACTCGGTTTGTTGGTGGGATTATCATGACCCATGGCGATGATG
upper sequence: GLYMA09G24670.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G52520.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------------------------------gtctgatgtactgtttttttta----------tat--atatatatt--tttaaatattaatataatccttttga----tgaggatgcagttgctcaaaatg-tgtgcttgtg----cagTTCACAGACGAAAATGGGTTAAGGGAATATGTTTGGCAGACATCATGGGCAATTAGTACACGTTTTGTTGGTGGCATCATCATGACACATGGAGATGATG
|| | | || |||||||| ||| | || | || | || | | || || ||||| | | ||| | ||||| || | || ||||| |||| || ||||| |||| || |||| |||||||||||||||||| | ||||||||||||||||||||||| |||||||| || ||||||||
gtacagaactattattgtctcacaagtatgtcatgcttatcgagacttgaatttgtttggagtttagttctctcatttttttagtgacgatagtattggtgcctactggttcatttagtcacatcttcgttttgcaacttcatcatgaaagaatgttaaatgacgtaatgatgatgccagTTTGCAGATGAGAATGGAGAAAGGCAACATGTGTGGCAGACATCATGGGCAGTCAGTACACGTTTTGTTGGTGGCATTATCATGACTCACGGAGATGACA
upper sequence: GLYMA09G24670.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 6
------gtctgatgtactgttttttttatatatatatatttttaaatattaatataatccttttgatgaggatgcagttgctcaaaatgtgtgcttgtgcagTTCACAGACGAAAATGGGTTAAGGGAATATGTTTGGCAGACATCATGGGCAATTAGTACACGTTTTGTTGGTGGCATCATCATGACACATGGAGATGATG
| | || || | | || || | ||| || | | | || || | ||| || |||| ||||||| ||||||| ||||||| || |||||||| ||| || | | |||||||||||||||||| | || || |||||| ||||||| ||||||||||| |||||||||||||
atttaatttttatttaagtagctctctacatgcgaacattatttttgttcatttcaa--ctatcaatggatatagtgttgaccaaaatgaatgcttgtatagTTCACTGATGAAAATGGACAAAGACAACACATATGGCAGACATCATGGGCAGTCAGCACCCGTTTTATTGGTGGTATCATCATGACCCATGGAGATGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaatataatccttttgatgaggatgcagttgctcaaaatgtgtgcttgtgcagTTCACAGACGAAAATGGGTTAAGGGAATATGTTTGGCAGACATCATGGGCAATTAGTACACGTTTTGTTGGTGGCATCATCATGACACATGGAGATGATG
tataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgatgtactgttttttttatatatatatatttttaaatattaatataatccttttgatgaggatgcagttgctcaaaatgtgtgcttgtgcagTTCACAGACGAAAATGGGTTAAGGGAATATGTTTGGCAGACATCATGGGCAATTAGTACACGTTTTGTTGGTGGCATCATCATGACACATGGAGATGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG