Sequence
atgc intronic sequence ATGC exonic sequencegtaaactcctttacctcttaaatccatagtaaagataattatcaattggtatcatttatgccactggaaggatgtcattttgagctcatcttaacatcgtaatgcttgttattgtagGAAGAGATAATCAATTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG
Basic information
species | Glycine max |
transcript | GLYMA09G23150.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 7
-------------------------------------------------------------------gtaaactcctttacctc--ttaaatccatagtaaagataattatcaattg-----gtatcatttatgccactggaagga--tgtcattttgagctcatcttaacatcgtaatgcttgttattgtagGAAGAGATAATCAATTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG
| ||| || |||| | || ||| || | | | ||| | ||| | | | | | |||||| | | ||| | || | | | | || | || || ||||||| || || | |||| | ||||||||||| ||||||||||| || || |||||||||||||| ||||||||||| |||||||||||| ||||||
gtatgatgcaatcgatcatattgctcgtactccattgtgctaacatgtccattacaacctgaggcttgaaaaagccattactttggttgtttccgtactttctagatctataatttgtccaggaaatagtcttcatgctggaatgcattaacatacaaacagcagtcttagaattttctgtgtcttcatgcagGAAGAAATTATTAGAATGTGCAGGAGCATGGGAAAAGCTGTTATTGTTGCCACTAATATGCTAGAAAGTATGATTGTTCATCCAACTCCAACCCGAGCAG
upper sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 7
gtaaactcctttacctcttaaatccatagtaaagataattatcaattggtatcatttatgccactggaaggatgtcattttgagctcatcttaacatcgtaatgcttgttattgtagGAAGAGATAATCAATTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG
| |||| | ||| | | | | || | | | | |||| || | | | ||| || | || || | || | ||| | || || ||||||| || || | |||| | |||||||| |||||||||||||| || ||||||||||| ||||| ||||||||||| |||||||||||| ||||||
------------agtgctta---ctataa-gctgtcagtaaagaaatattttttcctttgccgatgaaggtgtttcagatttacatcttccttgaat-attatgttctttcctgcagGAAGAAATTATTAGAATGTGCAGGAGCATGGGGAAGGCTGTTATTGTTGCTACAAATATGCTCGAAAGTATGATTGTTCATCCAACTCCAACCCGAGCAG
upper sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaactcctttacctcttaaatccatagtaaagataattatcaattggtatcatttatgccactggaaggatgtcattttgagctcatc-----ttaacatcgtaat----gcttgttattgtagGAAGAGATAATCAATTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG
| || | | | || || | || || | | |||| || || | | || || | || ||||||| |||| ||||| || || |||| ||||| |||||||| ||||||||||| || || || ||||| || || ||||| ||||| |||||||||||| | ||||
---------------------------------gttagtacttgcctctcatttttaagataacccagagaaggagatttagaacttgttgaagttgaaactcttgattttaatttgttat-acagGAGGAGATCATTAACCTGTGCCGTAGTATGGGAAAAGCTGTTATTGTTGCGACTAACATGCTTGAGAGTATGATAGTTCATCCAACTCCAACCCGGGCAG
upper sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 7
gtaaactcctt--tacctcttaaatccatagtaaagataatta-----tcaattggtatcatttatgccactggaaggatgtcattttgagctcatcttaacatcgtaatgcttgttattgtagGAAGAGATAATCAATTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG
|||| || || | | || || || || ||||||| || | || | || ||| | || ||||| | ||||| || | || ||||||||||||||| | ||||||||||||||||| ||||||||||| ||||| |||||||| ||||||||||||||||||||||| |||||| ||||||
gtaatttctttgtttctgattgaagagatgatagagataatagggtcttccagaagtgcctttcatgttttataacaagcatctacttgagtatttaccaacatttcaa--------actgcagGAAGAGATAATCAGGATATGTCGTAGCATGGGAAAAGCTGTTATTGTAGCAACCAATATGCTGGAAAGCATGATTGTTCACCCAACACCAACCCGAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actggaaggatgtcattttgagctcatcttaacatcgtaatgcttgttattgtagGAAGAGATAATCAATTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG
tcttaac putative branch site (score: 2)
ttgttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaactcctttacctcttaaatccatagtaaagataattatcaattggtatcatttatgccactggaaggatgtcattttgagctcatcttaacatcgtaatgcttgttattgtagGAAGAGATAATCAATTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG