Sequence
atgc intronic sequence ATGC exonic sequencegtgagtctaaaactgcatcactttttcctcttcctgaaatgagtggttcattatttttctcaattttgtcaatcctggggaccacattttcattattgaacttaataatatggcatgcagTGATTCTGTCCCCCTCTTTGGTTATCGAAGAAGGTCATACCTAGTTTTGTCAGGGCTGCTTGGTGCACTCTCGTGGAGTTTGATGGCTACTTTTGTTGAC
Basic information
species | Glycine max |
transcript | GLYMA20G28510.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G28510.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g07654.1 (Oryza sativa), 3'ss of exon 3
gtgagtctaaaactgcatcactttttcctcttcctgaaatgagtggtt-cattatttttctcaattttgtcaatcctggggaccacattttcattattgaacttaataatatggcatgcagTGATTCTGTCCCCCTCTTTGGTTATCGAAGAAGGTCATACCTAGTTTTGTCAGGGCTGCTTGGTGCACTCTCGTGGAGTTTGATGGCTACTTTTGTTGAC
|||| | || || | || | ||| | || | || | || || | | || | || ||| || | | ||||||||| |||| |||||||| |||||| ||||||||||||| || ||||||| | |||||||| || || ||| ||||||||||||| || || ||
---------------------------gtcttacaaaagctcctgcctacagttctttctgctatctgtacagtggtgta-actagaattctgctgtt---ctt-------tgcctttcagTGATTCCATCCCACTCTTTGGATATCGACGAAGGTCATACCTTATTCTGTCAGGATTCCTTGGTGCTCTTTCATGGGGTTTGATGGCTACATTGGTGGAT
upper sequence: GLYMA20G28510.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g58080.1 (Oryza sativa), 3'ss of exon 3
gtgagtctaaaactgcatcactttttcctcttcctgaaatgagtggttcattatttttctcaattttgtcaatcctggggaccacattttcattattgaacttaataatatggcatgcagTGATTCTGTCCCCCTCTTTGGTTATCGAAGAAGGTCATACCTAGTTTTGTCAGGGCTGCTTGGTGCACTCTCGTGGAGTTTGATGGCTACTTTTGTTGAC
|||| | | || | || |||| || | || | || || ||| | | || || || | | | ||| | | || | || ||||||||||| |||| |||||||| |||||||||||||| ||||| || | ||||| || || || || || ||||||||||||||||| || |||| ||
----gtctcag--caaaataccatatcttctttctaacat---tcttttatagtttatgtgtcacttatctat----gaagctatattgtt----tcgatttccat---------tgcagTGATTCCATCCCTCTCTTTGGATATCGAAGAAGGTCTTACCTTATTCTATCAGGACTCCTCGGAGCTCTTTCGTGGAGTTTGATGGCAACAATTGTGGAT
upper sequence: GLYMA20G28510.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G073429_T01 (Zea mays), 3'ss of exon 3
gtgagtctaaaactgcatcactttttcctcttcctgaaatgagtggttcattatttttctcaattttgtcaatcctggggac-cacattttcattattgaact--taataatatggcatgcagTGATTCTGTCCCCCTCTTTGGTTATCGAAGAAGGTCATACCTAGTTTTGTCAGGGCTGCTTGGTGCACTCTCGTGGAGTTTGATGGCTACTTTTGTTGAC
||| || ||| | || | || || ||| || | | | | || || | || ||| | || | | || ||||||||| |||| |||||||| |||||||||||||| |||||| || | ||||| | ||||| ||||| || |||||||||||||| || |||| ||
--------------------gtttcaccaaaataccgaataacctccctgccatccctttct-ttctgtatatgatatatgcacttaattgcaatgatgtactgtttttatttccgtatacagTGATTCCATCCCTCTCTTTGGATATCGAAGAAGGTCGTACCTATTTCTATCAGGCATCCTTGGAGCACTTTCATGGAGTTTGATGGCCGCTGTTGTGGAT
upper sequence: GLYMA20G28510.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G027603_T01 (Zea mays), 3'ss of exon 2
gtgagtctaaaactgcatcactttttcctcttcctgaaatgagtggttcattatttttctca-attttgtcaatcctg--gggaccacattttcattattgaacttaataatatggcatg-cagTGATTCTGTCCCCCTCTTTGGTTATCGAAGAAGGTCATACCTAGTTTTGTCAGGGCTGCTTGGTGCACTCTCGTGGAGTTTGATGGCTACTTTTGTTGAC
| || | | || || || | | | ||| | | | | ||||| || | | | | ||||||||| | || |||||||| ||||||||||||||||| || || |||||||| | ||||| ||||| || ||||| || ||||| || | || |
--------------------------------------------gtcccacaaatcctcccacatctaattctttctgatgtaggtgtacacttgattttgaatcctttactttcacctttcagTGATTCCATTCCACTCTTTGGATATCGAAGAAGGTCATATCTTTTTCTGTCAGGGTTACTTGGAGCACTTTCATGGAGCTTAATGGCCACAGTAGTGAGC
upper sequence: GLYMA20G28510.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G32040.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagtctaaaactgcatcactttttcctcttcctgaaatgagtggttcattatttttctcaattttgtcaatcctggggaccacattttcattattgaacttaataatatggcatgcagTGATTCTGTCCCCCTCTTTGGTTATCGAAGAAGGTCATACCTAGTTTTGTCAGGGCTGCTTGGTGCACTCTCGTGGAGTTTGATGGCTACTTTTGTTGAC
|| | ||| ||| | | | || || | | | ||| ||| || | || ||||||||||| || || || |||||||||||||| |||||||| |||||| | || || || ||||||||| | || ||||||||||||||| ||||||||||
---------------------------------------------gtatgagttctttatcacctctatacctcttgactgtgataactgt-ttaaggaagttggtc---tgttttgcagTGATTCAGTGCCTCTATTTGGTTATCGAAGGAGGTCATATCTAGTTCTCTCGGGACTTCTTGGTGCATTTTCTTGGAGTTTGATGGCTGGTTTTGTTGAC
upper sequence: GLYMA20G28510.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g03660.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtctaaaactgcatcactttttcctcttcctgaaatgagtggttcattatttttctcaattttgtcaatcctggggaccacattttcattattgaacttaataa-----tatggcatgcagTGATTCTGTCCCCCTCTTTGGTTATCGAAGAAGGTCATACCTAGTTTTGTCAGGGCTGCTTGGTGCACTCTCGTGGAGTTTGATGGCTACTTTTGTTGAC
||| ||||| | | |||| |||| | | || | ||| | | | |||| | ||| ||||||| ||| ||||| |||||| | || || |||||||||||||||||||||||| | ||| | |||||||| ||||| |||||||| |||||||||||||| |||||||| |||
-------------------gtgccggcctattcctttatc------tccattgttttcccttaattgataaatac-atgtttcctatttgtttatttgtgtttaataagtgtttatttattgcagCGATTCTTTACCACTTTTTGGTTATCGAAGAAGGTCATACTTGGTTCTATCAGGGCTTCTTGGAGCACTCTCATGGAGTTTGATGGCCACTTTTGTGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtcaatcctggggaccacattttcattattgaacttaataatatggcatgcagTGATTCTGTCCCCCTCTTTGGTTATCGAAGAAGGTCATACCTAGTTTTGTCAGGGCTGCTTGGTGCACTCTCGTGGAGTTTGATGGCTACTTTTGTTGAC
acttaat putative branch site (score: 4)
acattttcattattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtctaaaactgcatcactttttcctcttcctgaaatgagtggttcattatttttctcaattttgtcaatcctggggaccacattttcattattgaacttaataatatggcatgcagTGATTCTGTCCCCCTCTTTGGTTATCGAAGAAGGTCATACCTAGTTTTGTCAGGGCTGCTTGGTGCACTCTCGTGGAGTTTGATGGCTACTTTTGTTGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG