Sequence
atgc intronic sequence ATGC exonic sequence...attcatggtggttgttactttttgagtttaacttaatgtgttgtttgctttgttttttgagtaaattttgtggtgacattcttggttgttgtgtatgcagGCATAGATGGACTGGTAGATATGAAGCGCATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACCAGGAAAGGACGACAAG
Basic information
species | Glycine max |
transcript | GLYMA14G10130.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G10130.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 2
--------------attcatggtggttgttactttttgagtttaacttaatgtgttgtttgc-tttgttttttgagtaaattttgtggtgacattcttggttgttgtgtatgcagGCATAGATGGACTGGTAGATATGAAGCGCATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACCAGGAAAGGACGACAAG
||| ||| | || | | | | || | | || || | | || | | | | | | || | |||||||||| |||||||| |||||||| || || | ||||| ||||| |||||||||||||| || ||||| |||||||| ||||
gtagtagctagcagcgccatagtgacagacacctctcgccaccatgccgccatggcttccaccttcacagcttcacttaacctcaagtaaaaaaaccttgtaaa-----aagcagGCATAGGTGGACTGGGAGATATGAGGCACACCTCTGGGACAACAGCTGCAAGAAGGAAGGCCAGACCAGAAAAGGACGCCAAG
upper sequence: GLYMA14G10130.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 2
---attcatggtggttgttactttttgagtttaacttaatgtgttgtttgctttgttttttgagtaaattttgtggtgacattcttggttgttgtgtatgcagGCATAGATGGACTGGTAGATATGAAGCGCATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACCAGGAAAGGACGACAAG
||| ||| | | ||||| ||| | ||| ||| |||| | | |||| | | || | ||| || ||||||| || |||||||| ||||||||||| || | ||||||||||||||||| ||||| || || || ||||| ||| | ||||
tgtattgatgaggcacctactcttttgtttttgagcaaatcatttgacc-ctttttatattgaatgacgaaggtttgtgtgtgtttgatt--cactggagcagGCACAGGTGGACTGGAAGATATGAAGCCCACCTCTGGGATAACAGTTGCAAAAAGGATGGACAGACAAGGAAGGGAAGGCAAG
upper sequence: GLYMA14G10130.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G146688_T01 (Zea mays), 3'ss of exon 2
attcatg-gtggttgttactttttgagtttaacttaatgtgttgtttgc---tttgttttttgag-taaattttgtggtgacattc---------ttggttgttgtgtatgcagGCATAGATGGACTGGTAGATATGAAGCGCATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACCAGGAAAGGACGACAAG
| | | || | | | | || | | || || || | || | ||| | || | | ||| | | || || | || |||||||||| ||||| || || ||||| ||||| ||||||| ||||| |||||||||||||| || | |||||| || || ||||
gtacgtacgtacacgccgccgtgtcgagctagttgactggtccgtccgcccgtccgtccatggagctgaagctgaagttgaaactaaaactaaaactgaaagtaat-taagcagGCATAGGTGGACGGGGAGGTATGAGGCGCACCTGTGGGACAACAGCTGCAAGAAGGAAGGCCAGAGCAGGAAGGGCCGGCAAG
upper sequence: GLYMA14G10130.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G028151_T01 (Zea mays), 3'ss of exon 2
-------------------------attcatggtggttgttactttttgagtttaacttaatgtgttgtttgctttgttttttgagtaaattttgtggtgacattcttggttgttgtgta--tgcagGCATAGATGGACTGGTAGATATGAAGCGCATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACCAGGAAAGGACGACAAG
| | || | ||| | | | || | | || | |||| | ||| | | || ||| | |||||||||| ||||| || || ||||| ||||| | ||||| ||||| |||| |||||||||||| ||| ||||||| || ||||
gtatcctcccaactcccgaccgtccgtacgccgtcgctgtcgcaggc-gcgcgcgacccgcagcatccggcgcccgtgcgatcgagtcgctcac-tggccgcgtggtttcccaccgtgcaaaagcagGCATAGGTGGACGGGGAGGTATGAGGCGCACCTCTGGGACAACAGCTGCAGGAAGGAAGGGCAGACCCGGAAAGGCCGGCAAG
upper sequence: GLYMA14G10130.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
attcatggtggttgttactttttgagtttaacttaatgtgttgtttgctttgttttttgagtaaattttgtggtgacattcttggttg-ttgtgt-atgcagGCATAGATGGACTGGTAGATATGAAGCGCATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACCAGGAAAGGACGACAAG
||| ||||| | |||| || | | ||| || ||| ||| || || | ||| | || ||| | ||| |||||||||||||||||||||||||| ||| | ||||| || |||| |||||||||||| || | || |||||| ||||||
-------------gttgtttttttattttataatattaaact--ttgtttgactttcgttagtaatgttacatatacttacttaaaaggttatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
upper sequence: GLYMA14G10130.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------------------------------------attcatggtggttgttactttttgagtttaacttaatgtgttgtttgctttgttttttgagtaaattttgtgg---tgacattcttggttg-----------ttgtgtatgcagGCATAGATGGACTGGTAGATATGAAGCGCATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACCAGGAAAGGACGACAAG
| | || ||| | | | |||| || | | |||| | ||| | | |||| |||| | || ||| || || | | |||||||||||||||||||||||||||||| ||| | |||||||| |||||||||||||| ||||| || ||||||||| ||||||
gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctctattatattgtcctcgccttttctgctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctttgttttttgagtaaattttgtggtgacattcttggttgttgtgtatgcagGCATAGATGGACTGGTAGATATGAAGCGCATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACCAGGAAAGGACGACAAG
ttttttgagtaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attcatggtggttgttactttttgagtttaacttaatgtgttgtttgctttgttttttgagtaaattttgtggtgacattcttggttgttgtgtatgcagGCATAGATGGACTGGTAGATATGAAGCGCATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACCAGGAAAGGACGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - -tggtggt
- - - - -ggttgtt
- - - - - - - - - - - - - - - - - - tgtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtg