Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatttatgagcttttttattgtttttattttgtattattattattttttaaatatatcttgacaagttttatctgttgcagGTTCATGGCAACGTTTGCATGGCTAGTGTCGTTGTGACACCAACTTTGGACTGGAAGCTTCATGCTTTTGATGTTCTATCAGAGTTTGATGGGAGCAGTG
Basic information
species | Glycine max |
transcript | GLYMA18G47590.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47590.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 4
---gtgagtatttatg--agcttttttattgtttt-------tattttgtattattattattttttaaatatatcttgaca--agttttatctgttgcagGTTCATGGCAACGTTTGCATGGCTAGTGTCGTTGTGACACCAACTTTGGACTGGAAGCTTCATGCTTTTGATGTTCTATCAGAGTTTGATGGGAGCAGTG
|| ||||| || | | | || || | | | | || | | ||| ||| | |||| | | ||| || |||||||| || || || ||| || | || || ||||| || | |||| | || |||||||||||||||||||||||||| || || ||||||| | || |
catgttcttatttgtgcaaagtcatgtaatgacacacgaaaacaatgtatgttggaagttctttggtcataaaatttgaaattgtcatcatcaatttcagGTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGATTGGAAGCTTCATGCTTTTGATGTTCTTTCTGAATTTGATGCTAACAACG
upper sequence: GLYMA18G47590.1 (Glycine max), 3'ss of exon 4
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 4
------------gtgagtatttatgagcttttttattgtttttattttgtattattattattttttaaatatatc--ttgacaagttttatctgttgcagGTTCATGGCAACGTTTGCATGGCTAGTGTCGTTGTGACACCAACTTTGGACTGGAAGCTTCATGCTTTTGATGTTCTATCAGAGTTTGATGGGAGCAGTG
|| | ||| | | || | | | || || || | |||| ||| || || | |||||||||| || || ||| |||| ||||| ||||| |||| ||| |||| |||||||||||||||||||||||||| ||||| ||||||| | | ||
taaatcaaaacaatggggtcttaacacataattagaaagtacaacgctataaacgatttgattgtcaaatgacctgtttgccatcacttgatcaatatagGTTCATGGTAATGTATGCTTGGCCAGTGTTGTTGTTACACAAACCCTGGATTGGAAGCTTCATGCTTTTGATGTTCTGTCAGAATTTGATGCTAATAATG
upper sequence: GLYMA18G47590.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 4
-----------gtgagtatttatgagcttttttattgtttttattttgtattatta--ttattttttaaat-atatcttgacaagt-tttatctgttgcagGTTCATGGCAACGTTTGCATGGCTAGTGTCGTTGTGACACCAACTTTGGACTGGAAGCTTCATGCTTTTGATGTTCTATCAGAGTTTGATGGGAGCAGTG
||| | ||| | | | ||| || | | | | | | || || |||||| || | || ||| || | |||||||||| || || ||| | || ||||| ||||| |||| ||| |||| |||||||||||||| || |||||||| ||||| ||||||| | || ||
aaatcaaaacagtggggtcttaaca-cataattagaaattacaaatgatgtaaatgatttgattcttaaatgatctgtttgcaatcacttgatcaatatagGTTCATGGGAATGTATGCTTAGCCAGTGTTGTTGTTACACAAACCCTGGATTGGAAGCTTCATGCCTTCGATGTTCTGTCAGAATTTGATGCTAACAATG
upper sequence: GLYMA18G47590.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtatttatg---agcttttttatt--gtttttattttgtattattatt---------attttttaaatatatcttgacaagttttatctgtt--gcagGTTCATGGCAACGTTTGCATGGCTAGTGTCGTTGTGACACCAACTTTGGACTGGAAGCTTCATGCTTTTGATGTTCTATCAGAGTTTGATGGGAGCAGTG
|| ||||| | | | | | | ||| | | ||| | ||| | | |||||||| || | || ||||| || | ||||| ||||| || || || |||| ||||| ||||| ||||| |||||||||||||| || |||||| |||||||||||||||||||||||||||||| ||
gtaagtatctgtttataacactataattcagctattagagtatataaccggtggctagtcgattttttagttaaaactct-taagttctactgtcttaacagGTGCATGGTAATGTCTGTCTGGCAAGTGTTGTTGTTACACCTACTTTGGACTGGAAACTCCATGCTCTTGATGTTCTATCAGAGTTTGATGGGAGCAATG
upper sequence: GLYMA18G47590.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 4
------------gtgagtatttatgagcttttttattgtttttattttgtat-tattattattttttaaat-atatcttgacaagttttatctgttgcagGTTCATGGCAACGTTTGCATGGCTAGTGTCGTTGTGACACCAACTTTGGACTGGAAGCTTCATGCTTTTGATGTTCTATCAGAGTTTGATGGGAGCAGTG
|| | | | ||| | | | || | | ||| || || | | | | |||| || || || | ||||||||||| || |||||| |||| ||||| ||||| || | |||| ||||||||||||| ||||||||||| |||||||| ||||||||||| || |
tgctcctctggtgtcacacaccacaaaacaagttagaaatctattggtgcctctgatatcatgttggatgttactttctgacgagcattggcttctacagGTTCATGGTAATGTTTGCTTGGCCAGTGTTGTTGTCACTCAAACTCTGGACTGGAAGCTGCATGCTTTTGACGTTCTATCTGAGTTTGATGGCCATAGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttgtattattattattttttaaatatatcttgacaagttttatctgttgcagGTTCATGGCAACGTTTGCATGGCTAGTGTCGTTGTGACACCAACTTTGGACTGGAAGCTTCATGCTTTTGATGTTCTATCAGAGTTTGATGGGAGCAGTG
tcttgac putative branch site (score: 3)
ttttatct putative PPT
tattattattattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatttatgagcttttttattgtttttattttgtattattattattttttaaatatatcttgacaagttttatctgttgcagGTTCATGGCAACGTTTGCATGGCTAGTGTCGTTGTGACACCAACTTTGGACTGGAAGCTTCATGCTTTTGATGTTCTATCAGAGTTTGATGGGAGCAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG