Sequence
atgc intronic sequence ATGC exonic sequencegttgtaatatatttagtctaaatctcttttgttatgtttctctttggttctgttttttcacctttatttttagtttgttagtcattgtttttcttagaatcatcactggagtaatctgtttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCTCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC
Basic information
species | Glycine max |
transcript | GLYMA13G34970.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G027756_T02 (Zea mays), 3'ss of exon 5
gttgtaatatatttagtctaaatctcttttgttatgtttctctttggttctgttttttcacctttatttttagtttgttagtcattgtttttcttagaatcatcactggagtaatctgtttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCTCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC
| || | || | | | ||| ||||| | ||| |||| || ||| ||| ||||||||||||||||||| | || |||||||| ||||| ||||| || || || || || || || ||| |||| || |||||||| |||||||| ||||| |
-------------------------------------------------gtacttgtgcatttgctaaataaatttattagtagtgagcttttataga--caaggctgtttcaat--------gcagGCAGATATCTGGTCTTTAGGTATCACTGCCATTGAAATGGCTAAAGGTGAACCCCCTCTGGCAGATATTCATCCCATGAGAGTTCTTTTCATCATACCTC
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G53165.2 (Arabidopsis thaliana), 3'ss of exon 9
gttgtaatatatttagtctaaatctcttttgttatgtttctctttggttctgttttttcacctttatttttagtttgttagtcatt--gtttttcttagaatcatcactggagtaatctg--tttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCTCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC
||| | | | |||||||| | |||| || | | || | | || | ||| | || | | || || | || | |||| |||| ||||||||||| |||||||| ||||| || || ||||||||||| || || ||||| |||||||| ||||| || |||||||||||||| || || ||||
---gtatctcgtccatctgctgtagcttttgttgttcttctagtttacccaatcttct-gtgtataccctggctttacttgttttctagccctttctaattttgtcggtttctgcttctggtcttttccagGCAGATATATGGTCTCTTGGAATAACAATGATAGAGATGGCAAAAGGAGAACCTCCCCTTGCTGACCTTCATCCTATGAGAGTGCTTTTTATCATTCCCC
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G15220.1 (Arabidopsis thaliana), 3'ss of exon 9
gt-tgtaatatatttagtctaaatctcttttgttatgtttctctttggttctgttt---tttcacctttatttttagtttgttagtcattgtttttcttagaatc--atcactggagtaatctgtttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCTCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC
|| | | ||| || | || ||| | || || | || | ||| | || | | | |||| | | ||| ||| ||| | | |||| | | ||| || |||||||||| ||||| || ||||| || | |||||||||||||| || || ||||| || ||||| ||||| || |||||||||||||| || || || |
gtatctcgcctatatactgagcttcacttctcctagcttgacatgtgtgtttgtagaggctatacttgtttccttagcatatctaatattttttgccttctttttctgttgctgggattgt-tgtcatt-tagGCAGATATTTGGTCGCTCGGAATAACAGTTATTGAGATGGCAAAAGGAGAACCTCCCCTAGCTGACCTTCATCCCATGAGAGTGCTTTTTATCATTCCTC
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 9
gttgtaatatatttagtctaaatctcttttgttatgtttctctttggttctgttttttcacctttattt-ttagtttgttagtcattgtttttcttagaatcatcactggagtaatctgtttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCTCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC
| || | | | | || |||| ||||| || | ||| | |||| | | | | | || || | || | ||||||| ||||| |||||||||||||| |||||||||||||||||||| ||||||||||||||||| ||||| || ||||||||||||||||| || ||||| |
--------------------------tgaggtggtcagtatttgtgtttctccttttttgccatgttttgtccatttggtgcttcctcccacttctgatattattgggccatgaa--caatgatgcagGCGGATATTTGGTCTCTGGGAATAACTGCAATTGAGATGGCAAAAGGGGAGCCTCCACTTGCAGATCTCCATCCAATGAGAGTGCTTTTTATAATACCTC
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 8
gttgtaatatatttagtctaaatc--tcttttgttatgtttctctttggttctgttttttcacctttatttttagtttgttagtcattgtttttcttagaatcatcactggagtaatctgtttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCTCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC
||||| ||||||| | ||| | || | | | | ||| || ||| |||| || || | | | |||| | | | | | | | | | | || |||||||||||| ||||| ||||||||||||| ||||| ||||| || ||||| || || ||||||| | ||||| ||| | ||||| || | || |||
---gtaat-tatttaggttgtatcgacccttcgcttagaggagtaccgactcttcttcttcctcttt-ttcttcttattcttgtcaatactccttcaatagctgaaagcagtgcgttttatt---gcagGCAGATATATGGTCATTGGGAATCACTGCCATTGAAATGGCGAAAGGGGAACCACCTTATGCTGATTTACACCCTATGCGGGTGCTCTTTCTAATTCCCA
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S84_190V6.1 (Physcomitrella patens), 3'ss of exon 7
gttgtaatatatttagtctaaatctcttttgttatgtttctctttggttctgttttttcacctttatttttagtttgttagtcattgtttttcttagaatcatcactggagtaatctgttt---ttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCC---TCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC
|| | || || ||| | | | | | || | || ||||| | ||| | ||| ||| ||| || | || |||||||||||||| || || ||||||||||||| |||||||||||||| ||||| | | | | ||| ||
---------------------------ttcacttcccgtcgtttgtgttgaagaggatgatggt-agtgataaaaagctattcatttgtattccttcaat-atc-tgagagcaagtggcttgcattgcagGCAGATATATGTTCATTGGGAATCACTGCTATTGAGATGGCAAAAGGGGAACTGTATTCTCCAAGAGATTTT-------------------------------
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S59_173V6.1 (Physcomitrella patens), 3'ss of exon 7
gttgtaatatatttagtctaaatctcttttgttatgtttctctttggttctgttttttcac-----ctttatttttagtttgttagtcattgtttttcttagaatcatcactgg--agtaatctgtttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCTCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC
||| | || |||| | | | || | | | || | | ||||| | ||| | ||| | || || | | |||||||||||||| ||||| |||| ||||| || |||||||||||||| |||||||| || || ||||| || || ||| | || ||||| |||| ||
---------------------------------atgctactttttgctcattcgtgttgaagggggttatgcttgtgatggaaagatcattctcattcattcaatagctgagagcaggtgattt-tcattgcagGCAGATATATGGTCATTGGGGATCACCGCTATTGAGATGGCAAAAGGGGAGCCACCTTACGCAGATCTGCATCCTATGCGTGTTCTTTTTCTTATTCCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgttagtcattgtttttcttagaatcatcactggagtaatctgtttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCTCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC
tctgttttt CT-rich tract
attgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtaatatatttagtctaaatctcttttgttatgtttctctttggttctgttttttcacctttatttttagtttgttagtcattgtttttcttagaatcatcactggagtaatctgtttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCTCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT