Sequence
atgc intronic sequence ATGC exonic sequencegtcaagctatggaatatcaatcaggcaatcagaccgaacattctttagcttgttttatgtgtttaatctagatgcatgatggattgtttccctcacatgtgcttttactgcagGGAGTTAGTGTTGGTACCATCAAAACAAAGGCAAATGTGTGTTGTGTTCAGTTTCCCCTTGATTTTGCTCATTTCCTTGCATTTGGTTCAGCAGATCACC
Basic information
species | Glycine max |
transcript | GLYMA06G37080.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G37080.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G15354.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcaagctatggaatatcaatcaggcaatc----------agaccgaacatt-----ctttagcttgtttt-------------atgtgtttaatct--agatgcatgatggattgtttccctcacatgtgcttttactgcagGGAGTTAGTGTTGGTACCATCAAAACAAAGGCAAATGTGTGTTGTGTTCAGTTTCCCCTTGATTTTGCTCATTTCCTTGCATTTGGTTCAGCAGATCACC
|| ||||| |||| ||||||||||||||| | || ||| || | || ||| | | || | ||| ||| ||||| | |||| | | || | | | ||||||||||| |||| |||||||| |||||||| ||||| || ||||| |||||||| || | | | | || ||||||||||| ||||||||
gttaagctctggagtatcaatcaggcaattctaatttgaaatgtcggctattgaaaactgaaactgatttctacaataatgcaaacatcttcattctcagaatgtatgattaagagtttgtttttcttggaaatgtttt-cagGGAGTTAGCATTGGGACCATCAAGACAAAGGCCAATGTATGCTGTGTCCAGTTTCCATCAGACTCCGGACGGTCTCTAGCATTTGGTTCTGCAGATCATA
upper sequence: GLYMA06G37080.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G53090.2 (Arabidopsis thaliana), 3'ss of exon 4
gtcaagctatggaat--atcaatcaggcaatcagaccgaacattctttagcttgttttatgtgtttaatctagatgcatgatggattgtttccctcacatgtgcttttactgcagGGAGTTAGTGTTGGTACCATCAAAACAAAGGCAAATGTGTGTTGTGTTCAGTTTCCCCTTGATTTTGCTCATTTCCTTGCATTTGGTTCAGCAGATCACC
||| || | || | | | | | | | | | | | | ||| | ||| | |||| | | | ||| || | | | | | | ||||| |||||| |||| |||||||| ||||||||||| | ||||||||||||||||| || | || | | |||||||| ||||||||||||
-gcaaacttcgaaactaaaccaaaacgtatttatgctcggaaatgcgagaatagttct-----tttgag--ggatgtgtttttaacggttgagttcg--ttttcctctgtttcagGGGGTTAGTATTGGAACCATCAAGACAAAGGCAAACATATGTTGTGTTCAGTTTCCATCAGAGACGGGTCGGTCTTTAGCATTTGGCTCAGCAGATCACA
upper sequence: GLYMA06G37080.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv19s0014g02660.t01 (Vitis vinifera), 3'ss of exon 5
gtcaagctatggaatatcaatcaggcaatcagaccgaacattctttagcttgttttatgtgtttaatctagatgcatgatggattgtttccctcacatgtgcttttactgcagGGAGTTAGTGTTGGTACCATCAAAACAAAGGCAAATGTGTGTTGTGTTCAGTTTCCCCTTGATTTTGCTCATTTCCTTGCATTTGGTTCAGCAGATCACC
|||| | | || | ||| ||| | | | | || | | || ||| |||| || || |||||| || ||||| | | ||||||||||||| |||||||||||||||||||| ||||| ||||| || |||||||||||| ||| || | || | || |||||| ||||||||||| |||||
gtcagctttgaaactaaacgtactgcagtcat-ctaattacagtcgtgcatatggaat--------tctggatgtataataagttgtttttcttacatgggttgctactgcagGGAGTAAGTGTTGGTACCATCAAAACGAAGGCCAATGTATGCTGTGTTCAGTTTACCCCAGACTCTGGCCGTTACCTTGCTTTTGGTTCAGCTGATCATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtttaatctagatgcatgatggattgtttccctcacatgtgcttttactgcagGGAGTTAGTGTTGGTACCATCAAAACAAAGGCAAATGTGTGTTGTGTTCAGTTTCCCCTTGATTTTGCTCATTTCCTTGCATTTGGTTCAGCAGATCACC
ccctcac putative branch site (score: 3)
cttttact putative PPT
taatcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaagctatggaatatcaatcaggcaatcagaccgaacattctttagcttgttttatgtgtttaatctagatgcatgatggattgtttccctcacatgtgcttttactgcagGGAGTTAGTGTTGGTACCATCAAAACAAAGGCAAATGTGTGTTGTGTTCAGTTTCCCCTTGATTTTGCTCATTTCCTTGCATTTGGTTCAGCAGATCACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA