Sequence
atgc intronic sequence ATGC exonic sequence...ctgttcaggtagagaacatgcaaactgaaaaaagaaagttgatttttttaatgagctattatataatctttcttatacatgtcgattttaaattaatcagGCAAAGAGGGCAGGTTCAAAGCTGAAAAGCCGCATTGTTGCCGAGCAATCTATACATAAGTGGTCTCATATAATTGAGCAAATGGAAGACCAAATTTCTG
Basic information
species | Glycine max |
transcript | GLYMA18G11950.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G11950.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os12g29660.1 (Oryza sativa), 3'ss of exon 12
ctgttcaggta-gag-aacatgcaaactgaaaaaagaaagttgattttt--ttaatgagctattatataatctttcttatacatgtcgattttaaattaatcagGCAAAGAGGGCAGGTTCAAAGCTGAAAAGCCGCATTGTTGCCGAGCAATCTATACATAAGTGGTCTCATATAATTGAGCAAATGGAAGACCAAATTTCTG
| | ||| ||| | || ||| | | || | |||||| || | || | | | | || ||||| | | || | ||||||||||| || |||||| |||||||||| ||||||||||| ||| | || | | |||| | | | |||||| || | ||||| |||||||||
----taatgtatgagcattattgtgactatgatgatcaatgttatttttcgtttagccactgcttttgattgttacttattggtattcgttgaattgctttcagGCAAAGAAAGCTGGTTCACAGCTGAAAAGTCGCATTGTTGCAGAGAAGCCTGTGGCTGAGTGTGCAAAATTGATTGAGGAACTTGAAGATCAAATTTCTA
upper sequence: GLYMA18G11950.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G420865_T01 (Zea mays), 3'ss of exon 12
-ctgttcaggtagagaacatgcaaactgaaaaaagaaagttgatttttttaa-tgagctattatataatctttcttatacatgtcgattttaaattaatcagGCAAAGAGGGCAGGTTCAAAGCTGAAAAGCCGCATTGTTGCCGAGCAATCTATACATAAGTGGTCTCATATAATTGAGCAAATGGAAGACCAAATTTCTG
|||| | | | | || | || | | | ||| | | | || || | | ||| || ||||||||||| ||| |||||| |||||||||| ||||||||||| ||| || || | | |||| | | | ||||||||| | |||| ||||||||||
tttgtttttatcctttccctagaccctactcatgtggagcttccgacactgggtctgctctcggttgttgcttattggttttatttggcttacctt--tcagGCAAAGAAGGCTGGTTCACAGCTGAAAAGTCGCATTGTTGCAGAGAAACCTGTGGCTGAGTGTGCACGACTGATTGAGCAACTAGAAGGCCAAATTTCTA
upper sequence: GLYMA18G11950.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM5G804064_T01 (Zea mays), 3'ss of exon 12
-------ctgttcaggtagagaacatgcaaactgaaaaaagaaagttgatttttttaa--tgagctattatataatctttcttatacatgtcgattttaaattaatcagGCAAAGAGGGCAGGTTCAAAGCTGAAAAGCCGCATTGTTGCCGAGCAATCTATACATAAGTGGTCTCATATAATTGAGCAAATGGAAGACCAAATTTCTG
||| || || | | | || || ||||||| || | | || || || || |||| | || | | ||||||||||| ||| |||||| | |||||||||||||||||||| ||| || || | | |||| | || | ||||||||| | ||||| || |||||
cagaaatacactcatctattgatctgtcgagctcttctgagttttggtgtttttttggcctgggttgttgcttattcgtt-ttat-----ttgacct---acctttcagGCAAAGAAGGCTGGTTCACAACTGAAAAGCCGCATTGTTGCAGAGAAACCTGTGGCTGAGTGTGCACAACTGATTGAGCAACTAGAAGATCAGATTTCCA
upper sequence: GLYMA18G11950.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv18s0001g14540.t01 (Vitis vinifera), 3'ss of exon 12
ctgttcaggtagagaacatgcaaactgaaaaaagaaagttgatttttttaatgagctattatataatctttcttatacatgtcgattttaa---attaatcagGCAAAGAGGGCAGGTTCAAAGCTGAAAAGCCGCATTGTTGCCGAGCAATCTATACATAAGTGGTCTCATATAATTGAGCAAATGGAAGACCAAATTTCTG
| | || ||| || | ||| || | || | | | | ||||| || | |||| ||||| || ||||||||||||| ||||| |||||||| |||||||||||| ||||||||||||||| ||||| ||||||||||| ||| || |||
---tggtgttaatgaaattgaactgggaacctcctccaccccacccccaaaccccttgccatttgaggcaggcctcaagagcttcctttaatcgatgtaacagGTGAAGAGAGCTGGTTCAAAGCTGAGGAGCCGAATTGTTGCAGAGCAATCTATAATTAAGTGGTCTCATATGATTGAACAAATGGAAGATCAAGTTGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaatgagctattatataatctttcttatacatgtcgattttaaattaatcagGCAAAGAGGGCAGGTTCAAAGCTGAAAAGCCGCATTGTTGCCGAGCAATCTATACATAAGTGGTCTCATATAATTGAGCAAATGGAAGACCAAATTTCTG
ttttaat putative branch site (score: 3)
tattatataatctttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgttcaggtagagaacatgcaaactgaaaaaagaaagttgatttttttaatgagctattatataatctttcttatacatgtcgattttaaattaatcagGCAAAGAGGGCAGGTTCAAAGCTGAAAAGCCGCATTGTTGCCGAGCAATCTATACATAAGTGGTCTCATATAATTGAGCAAATGGAAGACCAAATTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - -acatgca
- - - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgtc