Sequence
atgc intronic sequence ATGC exonic sequence...tcatctgattttttcttatcagagatcatagccttctaactatgcaataatatgtttagtccttccctaattctttactctttgcgcccaaacttgacagCTAGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATATGTGGAGCTGA
Basic information
species | Glycine max |
transcript | GLYMA19G31730.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 2
tcatctgattttttcttatcagagatcatagccttctaactatgc--aataatatgttt---agtccttccctaattctttactctttgcgcccaaacttgacagCTAGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATATGTGGAGCTGA
| | | | | | || | | || | | ||||| | ||| |||| || | | || | | | | || | || | | |||| | || || |||| ||||| ||||||||||| || || || ||||| |||||||| ||||| || || ||||| ||||| | ||||||||||||||
ttaacggccgagtgttcatgcttggtttta-cttcttaactgttttgaattatatccttccaatttatttctgcaatttatatttgttttgttt----tctgcagCGGGGGTTCCATTGGAAAACATTCTTTATCTTGGAGGCCCTAACATTGCTTCAGAAATTTACAATAAAGAATATGCAAATGCTCGTATATGTGGAGCTGA
upper sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G090747_T02 (Zea mays), 3'ss of exon 2
tcatctgattttttcttatcagagatcatagccttctaactatgcaataatatgtttagtccttccctaattctttactctttgcgcccaa--acttg------acagCTAGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATATGTGGAGCTGA
||| | ||| || | ||| |||| | ||| || |||| || || | ||| | || ||| | | | | ||||| |||| || ||||| || ||||||||||| || || |||||||| || ||||| |||||||| || ||||| |||||| | || |||||||||||
-----agatacatatatatgctcaatgctt-cctcctaatc-tccaagtatttgtt-gtcccctctttgattttgtatgatttattatggactattggtataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTTCTGAAATTTACAACAAAGAATATGCAAATGCACGTATTTGTGGAGCTGA
upper sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
----------tcatctgattttttcttatcagagatcatagccttctaactatgcaataatatgtttagtccttccctaattctttactctttgcgcccaaacttgacagCTAGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATATGTGGAGCTGA
|| ||| |||| || | | || || || | || |||| || ||||| ||| |||| || | || | || |||| | ||||| || || || | || ||||||||||| ||||| ||||| | ||||| ||||||||||| ||||||||||| ||||| ||||||||||
gtaagctttttcttcttccttttgctccttttatattg-agtctattgac---acaat--cttgcttagtt-ttcttgaattggttcttactttggtgtt--tgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
upper sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------------------tcatctgattttttcttatcagagatc-atagccttct---aac-tatgcaataatatg----tttagtccttc--cctaattctttactctttgcgcccaaacttgacagCTAGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATATGTGGAGCTGA
| | || || || || | | || ||| |||| ||| | ||| ||| | | |||| | || |||| |||| | | | || || | ||||| | || ||||||| ||||| ||||| ||||| || ||||| ||||||||||| || ||||||||||||||||| ||||| ||||||||||||||||
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttt--tttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
upper sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S323_18V6.2 (Physcomitrella patens), 3'ss of exon 3
tcatctgattttttct-tatcagagatcatagccttctaactatgcaataatatgtttagtccttccctaattctttactctttgcgcccaaacttga--cagCTAGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATATGTGGAGCTGA
||| || | | | | ||||| | | | || | | | | ||||| | | ||| | |||| ||| || | ||| |||| |||||||| ||||| | || |||||||| |||||||||||||| || ||| | || ||||||||||| ||||||||| | || ||||| | ||
tcacttgtgtgtgtatgtatcatctaat-tggtttttttaaaaagtg-taataagatgagttgcttgagaattgca-actgactggtgggggatgtgattcagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTTCTGAAGTTTATAACAAGGAGTACGCCAATGCACGGATCTGTGGGTCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataatatgtttagtccttccctaattctttactctttgcgcccaaacttgacagCTAGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATATGTGGAGCTGA
ccctaat putative branch site (score: 3)
taattcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatctgattttttcttatcagagatcatagccttctaactatgcaataatatgtttagtccttccctaattctttactctttgcgcccaaacttgacagCTAGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATATGTGGAGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
-catctga
- - - - - - - - - - - - - - - gccttct
- - - - - - - - - - - - - - - - - - - -ctatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcgccca