Sequence
atgc intronic sequence ATGC exonic sequencegtcactccttgaacaccctacccttatcagaacattgttgattgattaggttcctcaaatttcattttttagtgataattctgttggtgcagGTCAAAAGGCACTGGTTTTCTTACATGGATTCCCAGAAATATGGTATACATGGAGGCACCAGATGATTGCTGCAGCAAATGCTGGCTACCGGGCTATTGC
Basic information
species | Glycine max |
transcript | GLYMA13G37430.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G37430.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g35490.2 (Oryza sativa), 3'ss of exon 1
--gtcactccttgaacaccct-acccttatcagaacattgttgattgattaggttcctc----aaatttcattttttagtgataattctgttggtgcagGTCAAAAGGCA---CTGGTTTTCTTACATGGATTCCCAGAAATATGGTATACATGGAGGCACCAGATGATTGCTGCAGCAAATGCTGGCTACCGGGCTATTGC
| | || | || | ||||| | | || || || | || || | | | || | | | ||| ||| | ||||| || ||| ||| | ||| | ||||| ||||| || | ||||| |||||||||||||||||||||| |||||| || || | ||| |||||
gtctgaatcttacctcatttttgttgacatcagcatctctctgcttttttttgctcttccgaaagaatgcagctcagcttcttgatttggttattccagGTGAAGCTGCAACTCTGCTCTTCGTTCATGGCTTCCCTGAGGTGTGGTACTCATGGAGGCACCAGATGATTGCAGCAGCAGCAGCCGGGTTCCGTGCTAT---
upper sequence: GLYMA13G37430.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0059g00210.t01 (Vitis vinifera), 3'ss of exon 1
gtcactccttgaacaccctacccttatcagaacattgttgattgattaggttcctcaaatttcattttttagtgataattctgttggtgcagGTCAAAAGGCACTGGTTTTCTTACATGGATTCCCAGAAATATGGTATACATGGAGGCACCAGATGATTGCTGCAGCAAATGCTGGCTACCGGGCTATTGC
| || | ||| | || | | ||| | || || | | | || || || | ||||||||| || || || | ||||| ||||| || || ||||||||||| ||||||||||||| ||| ||||||| ||| |||||||||||| || |||||
--------gtaaagaataaaccat-----aggttctgat-accaattgaaataaacatatatgaact--taaaagaaaatcaat--gtgcagGTCCTAAAGCGGTGCTGTTCTTGCATGGCTTTCCTGAAATATGGTACTCATGGAGGCACCAAATGGTTGCTGCTGCAGCTGCTGGCTACCGAGCAATTGC
upper sequence: GLYMA13G37430.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0059g00220.t01 (Vitis vinifera), 3'ss of exon 2
gtcactccttgaacaccctacccttatcagaacattgttgattgattaggttcctcaaatttcattttttagtgataattctgttggtgcagGTCAAAAGGCACTGGTTTTCTTACATGGATTCCCAGAAATATGGTATACATGGAGGCACCAGATGATTGCTGCAGCAAATGCTGGCTACCGGGCTATTGC
| ||| || ||| | | | || || || || || | | |||| | | || || | ||||||||| |||| || | ||| | ||||| ||||| |||||||||||| ||||||||||||| ||| |||| || ||| ||||| ||| | || |||||
---gtgaagaacaaaccttatgctt-tgacaccactggaagttactttaattttgta---tccattcctctaaaagaagtccct--gtgcagGTCCTAAGGTGGTGCTGTTCCTGCATGGTTTCCCTGAAATATGGTATTCATGGAGGCACCAAATGGTTGCCGCTGCAGCCGCTGGATACAGAGCAATTGC
upper sequence: GLYMA13G37430.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0059g00230.t01 (Vitis vinifera), 3'ss of exon 1
gtcactccttgaacaccctacccttatcagaacattgttgattgattaggttcctcaaatttcattttttagtgataattctgttggtgcagGTCAAAAGGCACTGGTTTTCTTACATGGATTCCCAGAAATATGGTATACATGGAGGCACCAGATGATTGCTGCAGCAAATGCTGGCTACCGGGCTATTGC
| ||| || ||| | | | |||| || || || | | | || | | || || | |||||||| |||| || | ||| | ||||| ||||| |||||||||||| ||||||||||||| ||||||||||| ||| |||||| ||||| || |||||
---gtgaagaacaaaccttatgctt-tgacaccatttgaagttactttaatttttttgcatcctttaatctaaaagaagtcactc--tgcagGTCCTAAGGTGGTGCTGTTCCTGCATGGTTTCCCTGAAATATGGTATTCATGGAGGCACCAAATGATTGCTGCTGCAGCTGCTGGATACCGAGCCATTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattgattaggttcctcaaatttcattttttagtgataattctgttggtgcagGTCAAAAGGCACTGGTTTTCTTACATGGATTCCCAGAAATATGGTATACATGGAGGCACCAGATGATTGCTGCAGCAAATGCTGGCTACCGGGCTATTGC
gattgat putative branch site (score: 4)
ttctgtt putative PPT
aaatttcattttttag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcactccttgaacaccctacccttatcagaacattgttgattgattaggttcctcaaatttcattttttagtgataattctgttggtgcagGTCAAAAGGCACTGGTTTTCTTACATGGATTCCCAGAAATATGGTATACATGGAGGCACCAGATGATTGCTGCAGCAAATGCTGGCTACCGGGCTATTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG