Sequence
atgc intronic sequence ATGC exonic sequencegtatggaactatcattgtcttctataacatggaattattaatatttgattgaaactgaaagcttactaacttctgtctagGTTGCTAAAGAATATTGTGAACAATTGGGCGTTGATGCTTGCATAAAGCTTTTTGAGCAGTTCAGGTCATATGAAGGGCTGTATTTTTTCCTGGGATCAT
Basic information
species | Glycine max |
transcript | GLYMA18G02960.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 17
------------------gtatgga-actatcattgtcttctataacatggaattattaatatttgattgaaact---gaaagcttactaacttctgtctagGTTGCTAAAGAATATTGTGAACAATTGGGCGTTGATGCTTGCATAAAGCTTTTTGAGCAGTTCAGGTCATATGAAGGGCTGTATTTTTTCCTGGGATCAT
| | | | | | || ||| | | | | | | |||| | | | | | | |||| ||| |||||||||| ||||||| | || ||||||||||||||||| | ||||| || |||| || ||||| || || || |||||| ||||||| |
gtaaatattgctccgttcctgtaaacatttttgttccaccctactgctttccctcccctgttcaagtatataacttttgtcaaacctgtggcacatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 18
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 19
gtatggaactatcattgtcttctataacatggaattattaatatttgattgaaactgaaagcttactaacttctgtctagGTTGCTAAAGAATATTGTGAACAATTGGGCGTTGATGCTTGCATAAAGCTTTTTGAGCAGTTCAGGTCATATGAAGGGCTGTATTTTTTCCTGGGATCAT
| | ||| | ||| | ||||| | || |||| ||| | | | | || | ||| | || || || ||||| ||| | || |||||||| || || ||||| ||||||||||||| ||||||||||||||| || |||||||| || ||||
-------gcaagtggtgtatgatatgatg-aatcttattggttatt--ttgacactaacggtgtccatacaat--ttcagGCTTGCAAGGAGTACTGTGAGCAACTTGGTGTTGATGCATGTATTAAGCTCTTTGAGCAGTTCAAGTCATATGAAGGGCTATACTTTTTCCTAGGTTCAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 18
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 19
gtatggaactatcattgtcttctataacatggaattattaatatttgat-tgaaactgaaagcttactaacttctgtctagGTTGCTAAAGAATATTGTGAACAATTGGGCGTTGATGCTTGCATAAAGCTTTTTGAGCAGTTCAGGTCATATGAAGGGCTGTATTTTTTCCTGGGATCAT
||||| || | ||||| | ||| ||| | | ||| | ||| || ||| ||||| | | | ||| | ||| | || || || ||||| ||| | || |||||||| ||||| || || |||||||| |||| ||| || ||||||||||| |||||||| || ||||
gtatgtg-ctgt-attgt----tgtaagatgtgaattttattgtttaatgtgacactga---cgtgtccatgtctttgcagGCTTGCAAGGAGTACTGTGAGCAACTTGGTGTTGATGCATGCATTAAACTCTTTGAGCAATTCAAGTCGTACGAAGGGCTGTACTTTTTCCTAGGTTCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacatggaattattaatatttgattgaaactgaaagcttactaacttctgtctagGTTGCTAAAGAATATTGTGAACAATTGGGCGTTGATGCTTGCATAAAGCTTTTTGAGCAGTTCAGGTCATATGAAGGGCTGTATTTTTTCCTGGGATCAT
tactaac putative branch site (score: 0)
cttctgtct CT-rich tract
aattattaatatttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggaactatcattgtcttctataacatggaattattaatatttgattgaaactgaaagcttactaacttctgtctagGTTGCTAAAGAATATTGTGAACAATTGGGCGTTGATGCTTGCATAAAGCTTTTTGAGCAGTTCAGGTCATATGAAGGGCTGTATTTTTTCCTGGGATCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG