Sequence
atgc intronic sequence ATGC exonic sequence...atgttgttaaagtaatgtgttgtcaatgttttctctctctctctctttttttattctatctgtgaatgacacacgtgcatgcatgtgatcgcgcgagcagTTTGGAAGGAGTTAGAGAAGGAGAACAAGGAGTTCTTCGAGGCATACACGAGGAGCAGAGCAGAGAGAGCTTCGGAGAGAGAGACAAGGCAAAGGATCCA
Basic information
species | Glycine max |
transcript | GLYMA19G35810.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G35810.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g38680.1 (Oryza sativa), 3'ss of exon 2
atgttgttaaagtaatgtgttgtca-atgttttctctctctctctctttttttattctatctgtgaatgacacacgtgcatgcatgtgatcgcgcgagcagTTTGGAAGGAGTTAGAGAAGGAGAACAAGGAGTTCTTCGAGGCATACACGAGGAGCAGAGCAGAGAGAGCTTCGGAGAGAGAGACAAGGCAAAGGATCCA
| | || || ||| | | | | | || | | | | || || || || | | | || | | | | ||||| ||||||||| | ||||||||||||||||||||||||||| | |||| | | ||| || ||| | ||| ||||| | ||| |||||||
-tatattttaatctttgtatggctatgtatcttatgacagaagccggagatgtaatccatttgcattatctaaaaatatattttgatctttgtggcggcagTATGGAAGGAGCTGGAGAAGGAGAACAAGGAGTTCTTCGAGACCTACAACAAGGACAGGGCGGAGCGCAACATCGAGGCGGAGACGATGCAGCGGATCCA
upper sequence: GLYMA19G35810.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g62060.3 (Oryza sativa), 3'ss of exon 2
atgttgttaaagtaatgtgttgtcaatgttttctctctctctctctttttttattctatctgtgaat----gacacacgtgcatgcatgtgat-cgcgcgagcagTTTGGAAGGAGTTAGAGAAGGAGAACAAGGAGTTCTTCGAGGCATACACGAGGAGCAGAGCAGAGAGAGCTTCGGAGAGAGAGACAAGGCAAAGGATCCA
| || ||| || | || |||| | | | | | | | |||| || | | | | | | || | || | | ||||||| ||||||||| | ||||||||||||| |||||||||| | |||| || | || || |||| | | ||||||| ||| || ||
----tacgaatataagatgaatactccgtattctatatgacgatatctgctcattc-gtcgagaatttttcaatattttttcttgattatgctgtctgtgagcagTGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGAAGGGCCAAGGAGAGGAACCAGCGGAGAGCAAGAGCAGTAGTTCTTCACA
upper sequence: GLYMA19G35810.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G108723_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------------------atgttgttaaagtaatgtgttgtcaatgttttctc------tctctctctctttttttattctatctgtgaatgacacacgtgcatgcatgtgatcgcgcgagcagTTTGGAAGGAGTTAGAGAAGGAGAACAAGGAGTTCTTCGAGGCATACACGAGGAGCAGAGCAGAGAGAGCTTCGGAGAGAGAGACAAGGCAAAGGATCCA
| || |||| || | ||||| | || | | | | || || ||||||||| | ||| | | ||| | | || ||||| ||||||||| ||||||| ||||||||||||||||||||| | |||| | | | | | ||| | |||| ||||| | | ||||| |
gtaccggccgtactaccgtgcatatatactggacacgcgcacgcgttatgctttccttcccccgttcaaccatttctcgtttaccttccatgcataatatgct-tcaataatcgatcatagattatattgttgttgttctattctatcatttcatgtggtctgaaaaagcacacca-catgcatgcagTGTGGAAGGAGCTAGAGAAAGAGAACAAGGAGTTCTTCGAGACGTACAACAAGGACCGCGAGGAGCGGAAGGTGGAGGCGGAGACGATGGCGCGGATCGA
upper sequence: GLYMA19G35810.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G370044_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------atgttgttaaagt-aatgtgttgtcaatgttttctctctctctc-tctttttttattctatctgtgaatgacacacgtgca-tgcatgtgatcgcgcgagcagTTTGGAAGGAGTTAGAGAAGGAGAACAAGGAGTTCTTCGAGGCATACACGAGGAGC---AGAGCAGAGAGAGCTTCGGAGAGAGAGACAAGGCAAAGGATCCA
||| || | | || | | | | | ||| || | | | | | | || | || || | | | | || | || |||||| ||||||||| | ||||||||||||| ||||||||||||| | |||| || | || |||| || | ||| ||| | | | | |||
gtaggccgtaggcggcactcttgcaagcaagcgattaatcgagattatttcaagagtagttaagttgtcgtccacgccaaattaaagctactactagtcgactcgatcgtatcgatctcattgacctcttcttggcattattatactatacatgct-gctatagcagTGTGGAAGGAGCTGGAGAAGGAGAACAGGGAGTTCTTCGAGACGTACAAGAAGTATCTGGGACAAGAGTCGGCGCTGCAGA-AGAATCCATCCGATGGACA--
upper sequence: GLYMA19G35810.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G02580.1 (Arabidopsis thaliana), 3'ss of exon 2
atgttgttaaagta-atgtgttgtcaatgttttctctctctctctctttttttattctatctgtgaatgacacacgtgcatgcatgtgatcgcgcgagcagTTTGGAAGGAGTTAGAGAAGGAGAACAAGGAGTTCTTCGAGGCATACACGAGGAGCAGAGCAGAGAGAGCTTCGGAGAGAGAGACAAGGCAAAGGATCCA
||| | | || | || | | | | | | || | || | |||| || | || | || |||| ||||| ||||| ||| ||| ||| |||||||| |||||||||||||||||| ||| || ||| ||| | | | | |||| ||||||| | ||| ||||
-----------gtacacatattatagatagata-tatggtagtatggtacaatagta-atttatgaaagataagggttggagaat-tgattaaatttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGAGAAGACGAGAAGAAATACCGACCGAGAAAGAGACAGCTCGAAGAATCCG
upper sequence: GLYMA19G35810.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0040g02650.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------atgttgttaaagtaatgtgt-tgtcaatgttt-tctctctctctctctttttttattctatctgtgaatgacacacgtgcatgcatgtgatcgcgcgagcagTTTGGAAGGAGTTAGAGAAGGAGAACAAGGAGTTCTTCGAGGCATACACGAGGAGCAGAGCAGAGAGAGCTTCGGAGAGAGAGACAAGGCAAAGGATCCA
|| | || | || | | | | || | | | | | | | | | | || | || | | | | | | || || | | ||||| |||||||| || ||||| ||||||||||||||||||||| | ||| | | |||||||| | |||| ||| || | ||||||||| ||| ||||
gtcagcgattaccttctcaaactccataactatatatatatatatatatatatatatatatatatatatatttatacatatgcttgtcctctgcataacacgtatatgcatatatatcttgatgatactgcagTGTGGAAGGAATTGGAGAAAGAGAACAAGGAGTTCTTCGAGTCCTACGCAAAGAGCAGAGAGGCAAGAGGTTCTGATATGGAGACAAGGGAAAATTTCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttattctatctgtgaatgacacacgtgcatgcatgtgatcgcgcgagcagTTTGGAAGGAGTTAGAGAAGGAGAACAAGGAGTTCTTCGAGGCATACACGAGGAGCAGAGCAGAGAGAGCTTCGGAGAGAGAGACAAGGCAAAGGATCCA
ttattctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgttgttaaagtaatgtgttgtcaatgttttctctctctctctctttttttattctatctgtgaatgacacacgtgcatgcatgtgatcgcgcgagcagTTTGGAAGGAGTTAGAGAAGGAGAACAAGGAGTTCTTCGAGGCATACACGAGGAGCAGAGCAGAGAGAGCTTCGGAGAGAGAGACAAGGCAAAGGATCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
-tgttgtt
- - - - - - - - -tgttgtc
- - - - - - - - - - - - - - - - ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgca