Sequence
atgc intronic sequence ATGC exonic sequencegtattgagaacttgcattgcatcaaaacaggatttttttttcatgcccttgtagaattgatttttactatttccatcctttttgtttagCCTTGCATCATATTCATGGATGAGATTGATGCCATTGCTGGACGACGTTCCAGTAACCGCAAAGGTTCTGATCGTGAAATTCAAAGAACCCTCAAGGAGC
Basic information
species | Glycine max |
transcript | GLYMA06G01200.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G01200.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g40560.1 (Oryza sativa), 3'ss of exon 6
-----gtattgagaacttgcattgcatcaaaacaggatttttttttca-tgcccttgtagaattgatttttactatttccatc-----ctttttgtttagCCTTGCATCATATTCATGGATGAGATTGATGCCATTGCTGGACGACGTTCCAGTAACCGCAAAGGTTCTGATCGTGAAATTCAAAGAACCCTCAAGGAGC
|||| |||||| || | | || | || | ||| || | | |||| | ||| || | |||||||||||||| |||||||| ||||||||||| ||||||||||| | ||| ||| | | |||| | | | || |||| || |||||||| ||||| || | |||||
gtcatgtatatcatgtatgcatttgtccacttctctacttaataaccagtctacttatattaatcatttgtgctacttttgttttgaactttttgtttagCCATGCATCATTTTCATGGATGAAATTGATGCCATCGGTGGCCGAAGGTTCAGTGAAGGAACCAGTGCTGACCGGGAAATTCAGAGAACACTAATGGAGC
upper sequence: GLYMA06G01200.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G074037_T01 (Zea mays), 3'ss of exon 6
-----------gtattgagaacttgcattgcatcaaaacaggatttttttttcatgcccttg-tagaattgatttttactatttccatcctttttgtttagCCTTGCATCATATTCATGGATGAGATTGATGCCATTGCTGGACGACGTTCCAGTAACCGCAAAGGTTCTGATCGTGAAATTCAAAGAACCCTCAAGGAGC
| | || || || | || | | | | ||| | ||| || || || | | || ||| || ||| ||||| |||||||| ||||||||||| ||||||||||||| ||| ||| | | ||| | ||| | || | |||||||| ||||| || || | | |||||
acacccgtggcccgtgcataatttcttttaattgaagtgcataatccgtgtatatgtcattgctataaaatgttgtctttggttttatc-ttgttgcctagCCATGCATCATTTTCATGGATGAAATTGATGCCATTGGTGGCCGAAGATTTAGTGAGGGCACAAGTGCAGATCGTGAGATTCAGAGGACATTGATGGAGC
upper sequence: GLYMA06G01200.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G171604_T01 (Zea mays), 3'ss of exon 6
------------gtattgagaacttgcattgcatcaaaacaggatttttttttcatgcccttgtagaattgatttttactatttcca-tcctttttgtttagCCTTGCATCATATTCATGGATGAGATTGATGCCATTGCTGGACGACGTTCCAGTAACCGCAAAGGTTCTGATCGTGAAATTCAAAGAACCCTCAAGGAGC
| | || ||| || | || | | |||| || ||| | || | ||| ||||| || || | | || || | ||||| |||||||| ||||||||||| ||||||||||||| ||| ||| | | |||| | | | || |||||||||| || || | || | | ||| |
aatcactaacgcacttcccgtacctgccgtgtaccatcatccg-ttttagttccat-cactaatgatattagtttttttcatgtcaaattgttcttttctagCCATGCATCATCTTCATGGATGAAATTGATGCCATTGGTGGGCGAAGATTCAGTGAGGGAACTAGTGCTGATCGTGAGATCCAGCGGACGTTGATGGAAC
upper sequence: GLYMA06G01200.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------------------------gtattgagaacttgcattgcatcaaaacaggatttttttttcatgcccttgtagaattgatttttactatttccatcctttttgtttagCCTTGCATCATATTCATGGATGAGATTGATGCCATTGCTGGACGACGTTCCAGTAACCGCAAAGGTTCTGATCGTGAAATTCAAAGAACCCTCAAGGAGC
| || | ||| ||| ||| | | | | |||| | || | | |||| | |||| |||||||||||||||| |||||||||||||||||||||| || || |||| || | | | || | ||||| ||||| || | ||||| | ||||
gtactacctcttttcatctgcacttggttcagttcttccatattaaagtggttacaggagttacgcttttgttttgttgattaacctccaaaactgctaacgttgttgttgtggtggctactttgtggaccattatctttgc--agCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttcatgcccttgtagaattgatttttactatttccatcctttttgtttagCCTTGCATCATATTCATGGATGAGATTGATGCCATTGCTGGACGACGTTCCAGTAACCGCAAAGGTTCTGATCGTGAAATTCAAAGAACCCTCAAGGAGC
aattgat putative branch site (score: 4)
tttttactatttccat CT-rich tract
tagaattgatttttac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgagaacttgcattgcatcaaaacaggatttttttttcatgcccttgtagaattgatttttactatttccatcctttttgtttagCCTTGCATCATATTCATGGATGAGATTGATGCCATTGCTGGACGACGTTCCAGTAACCGCAAAGGTTCTGATCGTGAAATTCAAAGAACCCTCAAGGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG