Sequence
atgc intronic sequence ATGC exonic sequencegtatgattatattatgaaatgcctcatgcttttgtgaatgagtaaattactaaacatcattgctttttcagGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG
Basic information
| species | Glycine max |
| transcript | GLYMA05G26230.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g45820.1 (Oryza sativa), 3'ss of exon 2
---------------gtatgattatattatgaaatgcctcatgcttttgtgaatgag-------taa-attac---taaacatcattgcttttt---cagGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG
|| | | | | | ||| | | || || | || | ||| |||| || || | | ||| || ||||| | ||||||||||| ||| || | |||||||| || || || ||||| || | ||||||||| ||||| ||| ||||||| ||||||||||| || |
ttgagttatctttgagtgttctcaaagttagaattttgttatcctcatatgtccaaaaccttgctaacattatggatataccttttaacttgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTGCACGGTAGCAACAAGAAGTTCGATACTGATGTCTCTCTTGAAGTCATAG
upper sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G087598_T01 (Zea mays), 3'ss of exon 2
-----------------------------gtatgattatattatgaaatgcctcatgctt-ttgtgaatgagtaaattactaaacatcattgctttttcagGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG
|| ||| || ||||| | | || || | || | || | ||| || |||||| | || || ||||| ||| || | |||||||| || || ||||| || |||| ||||||||| || |||||| |||||||||||||||| || || |
ttcatctttcattcaatacctgaacactagttagatcttaacg-gaaatatatgggggttgttcttaacatctttggtatgccttgtaattcattacacagGTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTGCATGGTAGCAACAAGAAATTTGATTCTGATGTTTCTCTTGATGTCATAG
upper sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G087598_T03 (Zea mays), 3'ss of exon 2
-----gtatgattatat-tatgaaatgcctcatgcttttgtgaatgagtaaattactaaacatcattgctttttcagGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG
|| | | || | || || | | | | || | | || | | | | | ||| || | | || | ||||||| || || | ||| ||| || | | ||| | ||| || | || || | || |
tcgacgt-tcctgatgtacgtggaaggacaga-gattctaaaagtgcatgg-tagcaacaagaaatttgattctgatgtttctcttgatgtcatag---caatgagAACACCTGGGTTCAGCGGAGCAGACTTGGCAAACCTTCTGAATGAAGCAGCCATTCTGGCTGGAA-GACGG
upper sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 2
----------------------------gtatgattatattatgaaat-gcctcatgcttttgtgaatgagtaaattactaaacatcattgctttttcagGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG
| | | | || | || | | | | ||| | | || | ||| || |||||| | ||||||||||| ||| || | |||||||| || || ||||| || |||| | ||||||| || |||||| ||||||||||||| || || || |
ccatttggttcagcttgatccatctttattccgtacctgacactaattcgctgggggttgtccttaatatcttgagtatgccttaaaattcgttgcacagGTGTCTGTTGATGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTGCATGGTGGCAACAAGAAATTTGATTCTGATGTTTCTCTCGATGTCATAG
upper sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0028g01600.t01 (Vitis vinifera), 3'ss of exon 2
----gtat---gattatattatgaaatgcctcatgcttttgtgaatgagtaaattactaaacatcattgcttttt--cagGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG
| || || |||||| | ||||| || ||| | | | | || |||| | | | | ||||| ||||| || ||||||||||| |||||| |||||||||| || ||| |||||||||||||| | || || |||||||||| ||||| |||||||| || || |
gtaagcatagagaatatattgttttttgccttatcttttattataagtgggaaatactta-cgttaaagctttggagcagGTAACTGTTGATGTTCCTGATATACGGGGAAGGACAGAGATCTTAAAGGTTCATGCTGGTAATAAGAAGTTTGATGGAGATGTGTCTCTTGATGTAATAG
upper sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S118_166V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------gtatgattatattatgaaatgcctcatgcttttgtga-atgagtaaattactaaacatcattgcttt------------------ttcagGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG
|||||| | | |||| || | || | ||| || | | | | | | || ||||| | || |||||||| || | | |||||||||||| ||||| ||||| |||||||| ||||| ||||| | | |||||| ||||| || | ||||
gtaatgtcatgaaaccatgatttaaatttgaacaatcttcaatcctcatggtgtatctaacttgcaagatgttagtttcttaatgtggagacgacgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTGCATGCTAGTAACAAGAAGTTCGCCGATGATGTGTCTCTGGATATCATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgcctcatgcttttgtgaatgagtaaattactaaacatcattgctttttcagGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG
tactaaa putative branch site (score: 1)
ttgctttttc putative PPT
taaattactaaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgattatattatgaaatgcctcatgcttttgtgaatgagtaaattactaaacatcattgctttttcagGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
