Sequence
atgc intronic sequence ATGC exonic sequence...aaaagttaatagttataacttttatatctcaaacatgacttcttatttctttacgagtttctaaacacactatgatagacaatacatgttgtcatcacagGTGGTCGGTGATTGCAGCTCAATTGCCGGGAAGAACCGACAATGACATAAAGAACTACTGGAACACGAGGCTGAAAAAGAAGCTTCTGGGGAAGCACCGA
Basic information
species | Glycine max |
transcript | GLYMA0041S00310.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA0041S00310.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g56090.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------------aaaagttaatagttataacttttatatctcaaacatgacttcttatttctttacgagtttctaa-acacactatgata-gacaatac-atgttgtcat--cacagGTGGTCGGTGATTGCAGCTCAATTGCCGGGAAGAACCGACAATGACATAAAGAACTACTGGAACACGAGGCTGAAAAAGAAGCTTCTGGGGAAGCACCGA
| | ||| | | | | | || || | | | || | ||| | || ||| ||||||| |||| || || | ||| |||||||||||| | || ||||| || ||||||| | || ||||||||||| |||||||| |||||||||||||| || |||||||| | || |||||
gtatacttgctaattcagctgggcacacacaagtctagtcactcctatgatcaactcaactgtagaattagctgcgaaaccggtaggcaggcaggca-ggttgcacatggggc-atgagagtgtagtacaatctatgatctgacatgaccatatatgcatggcacagGTGGTCGATAATAGCAGCGCAGCTGCCGGGGCGGACGGACAATGACATCAAGAACTATTGGAACACGAGGCTCAAGAAGAAGCTCTTTGGCAAGCAGTCG
upper sequence: GLYMA0041S00310.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G104789_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------aaaagttaatagttataacttttatat----ctcaaacatgacttcttatttctttacgagtttctaaacacac-tatga--tagacaatacatgtt-gtcat-------cacagGTGGTCGGTGATTGCAGCTCAATTGCCGGGAAGAACCGACAATGACATAAAGAACTACTGGAACACGAGGCTGAAAAAGAAGCTTCTGGGGAAGCACCGA
| || || | | | || | | | | |||||| | | | | | | || ||||| | || || ||||| | ||||||||| | || || || || |||||||||| || ||||| ||||||||||||||||||||||||||||| || |||||||| | || |||||
gtaaagttcagtagctaggtcgtcctgacctggtgttttcttcgatcaaatccacacactgtagaatttgctggctgcaaaccaactgttaggcacgcacatgatgcatgggtgtgtgcccggccgtagagtctacctatgacctgaactgaacggaccagtcatgcatgcccgtagGTGGTCGATAATAGCGGCGCAGCTGCCGGGAAGGACGGACAACGACATAAAGAACTACTGGAACACGAGGCTCAAGAAGAAGCTCTTCGGCAAGCAGTCG
upper sequence: GLYMA0041S00310.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G104789_T02 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------aaaagttaatagttataacttttatat----ctcaaacatgacttcttatttctttacgagtttctaaacacac-tatga--tagacaatacatgtt-gtcat-------cacagGTGGTCGGTGATTGCAGCTCAATTGCCGGGAAGAACCGACAATGACATAAAGAACTACTGGAACACGAGGCTGAAAAAGAAGCTTCTGGGGAAGCACCGA
| || || | | | || | | | | |||||| | | | | | | || ||||| | || || ||||| | ||||||||| | || || || || |||||||||| || ||||| ||||||||||||||||||||||||||||| || |||||||| | || ||||
gtaaagttcagtagctaggtcgtcctgacctggtgttttcttcgatcaaatccacacactgtagaatttgctggctgcaaaccaactgttaggcacgcacatgatgcatgggtgtgtgcccggccgtagagtctacctatgacctgaactgaacggaccagtcatgcatgcccgtagGTGGTCGATAATAGCGGCGCAGCTGCCGGGAAGGACGGACAACGACATAAAGAACTACTGGAACACGAGGCTCAAGAAGAAGCTCTTCGGCAAGCCGTTT
upper sequence: GLYMA0041S00310.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G49690.1 (Arabidopsis thaliana), 3'ss of exon 2
aaaagttaatagttataacttttatatctcaaacatgac-ttcttatttctttacgagtttctaaacacactatgata-gacaatacatgttgtcatcacagGTGGTCGGTGATTGCAGCTCAATTGCCGGGAAGAACCGACAATGACATAAAGAACTACTGGAACACGAGGCTGAAAAAGAAGCTTCTGGGGAAGCACCGA
|| || | ||| |||| || | || | || || || | || ||| || | | | || || || | | || | |||||||| | || || ||||||||||||||| |||| ||||| || ||||| ||||| |||||||||||||| || ||||| || | || || ||
-----gtactattcatatacgttat-tcatgtatatatcgttaaaatatcatgtggaaactctgaa-atatagttatgtgatgatgt---ctataattaaagGTGGTCTATAATCGCTGCTCAATTGCCGGGACGAACAGACAACGATATAAAAAACTATTGGAACACGAGGCTCAAGAAGAAACTCATTAACAAACAACGC
upper sequence: GLYMA0041S00310.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G65790.1 (Arabidopsis thaliana), 3'ss of exon 2
aaaagttaatagttataacttttatatctcaaacatgact---tcttatttctttacgagtttctaaacacactat-gatagacaatacatgttg---tcatcacagGTGGTCGGTGATTGCAGCTCAATTGCCGGGAAGAACCGACAATGACATAAAGAACTACTGGAACACGAGGCTGAAAAAGAAGCTTCTGGGGAAGCACCGA
| | ||| ||| | | | ||| | |||| | | ||||| || || || | || || || || || || | || |||||||| | ||||| || ||||||||||||||||||||||| || || || ||||| ||||||||||||||||| |||||||||||| || || |
-gtactatatacttacatatatatcatcatatgcatggatgaatattattaattgacacacttattcttgacttagagactcactatgtatctttgtttaattctagGTGGTCTATAATTGCTGCACAATTGCCGGGAAGAACCGACAACGATATCAAAAACTATTGGAACACGAGGCTGAAGAAGAAGCTTCTGAACAAACAAAGG
upper sequence: GLYMA0041S00310.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g08470.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------aaaagttaatagtta--taacttttatatctca-------aacatgacttcttatttctttacgagtttctaaacacactatgatagacaatacatgttgtcatca-cagGTGGTCGGTGATTGCAGCTCAATTGCCGGGAAGAACCGACAATGACATAAAGAACTACTGGAACACGAGGCTGAAAAAGAAGCTTCTGGGGAAGCACCGA
| || ||| ||| | || ||| | ||| | | || || | | |||| || || | | || | | ||| |||| | ||||||||| || |||||||| ||||| || ||| |||| |||||||| ||||||||||||||||| ||||| ||||| |||||||| || || ||||| ||
gtgtgccctcaaaaatttaatgatgctcataactgtagatctgtatataattaaccatctcttagacctcttttgagtggtacaatgggttgattttacaggagtggct---catgttgtaatgaaacacttg-gttttcatgaacagGTGGTCTGTTATTGCAGCACAATTACCAGGACGAACTGACAATGATATAAAGAACTACTGGAATACGAGACTGAAGAAGAAGCTCCTTGGTAAGCAGCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctttacgagtttctaaacacactatgatagacaatacatgttgtcatcacagGTGGTCGGTGATTGCAGCTCAATTGCCGGGAAGAACCGACAATGACATAAAGAACTACTGGAACACGAGGCTGAAAAAGAAGCTTCTGGGGAAGCACCGA
ttctaaa putative branch site (score: 2)
tttctaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaagttaatagttataacttttatatctcaaacatgacttcttatttctttacgagtttctaaacacactatgatagacaatacatgttgtcatcacagGTGGTCGGTGATTGCAGCTCAATTGCCGGGAAGAACCGACAATGACATAAAGAACTACTGGAACACGAGGCTGAAAAAGAAGCTTCTGGGGAAGCACCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - -caaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacatgt