Sequence
atgc intronic sequence ATGC exonic sequence...gcataggttttgcctgttacacatcgtctatgttatatataaatttgattcatcaccagtttcccttgatgttatcattacagtttgaagtctactatagTGCCATTGTTTGAGAAGGTATTGAGTGCCAGTGATGCAGGTCGAATTGGTCGACTTGTTCTCCCAAAATCTTGTGCTGAG
Basic information
species | Glycine max |
transcript | GLYMA14G38490.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G38490.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G172621_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------------------------------------------------------gcataggttttgcctgttacacatcgtctatgttatatataa---atttgattcatcaccagtttcccttgatgttatcattacagtttgaagtctactatagTGCCATTGTTTGAGAAGGTATTGAGTGCCAGTGATGCAGGTCGAATTGGTCGACTTGTTCTCCCAAAATCTTGTGCTGAG
|| || | | | | || | | | || | | | ||| || | | | | |||||| ||| | |||| || || || || || ||||||||||||||||| ||||||| ||||||||||| || || || || |||||||| |||||| |||||||||||
gtatccttgataaggctttcatgcatttgaaattgtcaacttcctggtgacattgatctttgacatttagtaccttataaatacaaggctccagaagagctcattaggcttaagcct-gtataatatgctgcataaattctttttgtaacagatgcaggttttgttttatcttccttgactatattttggaagTTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCTGAG
upper sequence: GLYMA14G38490.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------------------------------------------gcat-aggttttgcctgttaca-catcgtctatg------ttatata-taaatttgattcatcaccagtttcccttgatgttatcattacagtttgaagtctactatagTGCCATTGTTTGAGAAGGTATTGAGTGCCAGTGATGCAGGTCGAATTGGTCGACTTGTTCTCCCAAAATCTTGTGCTGAG
||| ||| || | ||| | || | || || | || | || | || || | | |||||| ||| | |||| || || || || || |||||||| |||||||| ||||||| ||||||||||| || || || || |||||||| |||||| ||||||| |||
gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG
upper sequence: GLYMA14G38490.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G30470.1 (Arabidopsis thaliana), 3'ss of exon 4
gcataggtt--ttgcctgttacacatcgtcta--tgttatatataaatttgattcatcaccagtttcccttgatgttatca--ttacagtttgaagtctactatagTGCCATTGTTTGAGAAGGTATTGAGTGCCAGTGATGCAGGTCGAATTGGTCGACTTGTTCTCCCAAAATCTTGTGCTGAG
| || || |||| | | || | | | | || ||| || | | | | || || ||| || || |||||||| | | || || || | |||||||| | |||||||||||||| ||||| |||||||| || ||||| |||||| | ||||| |||
gtatcctttatttgcttctagtacttttgccaaatattttattctggacagacttctggtgactcattgtttatcttaacaaattctagTTTGAATTTGAACATTGTACCTCTCTTTGAGAAAACTCTTAGTGCCAGTGATGCTGGTCGCATTGGTCGTCTAGTTCTTCCAAAAGCCTGTGCAGAG
upper sequence: GLYMA14G38490.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g08100.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------gcata-ggttttgcctgttacacatcgtctatgtt-atatataaatttgattcatcaccagtttcccttgatgttatcattacagtttgaagtctactatagTGCCATTGTTTGAGAAGGTATTGAGTGCCAGTGATGCAGGTCGAATTGGTCGACTTGTTCTCCCAAAATCTTGTGCTGAG
| || | |||| | | || || | ||| | || ||| ||| | | | | |||||||| | | |||||||| || || || |||||||| || |||||||| ||||||| |||||||| |||||||||||||| | || ||||||||| | ||||||||
gtatccataaatatttcatactttaatttttaagttgattatcatcataatagaatgtgattttatgtaacattcaatgtgttggtttgttcattgattcaattaagtgtttaccttacat-atgttatcttca-agTTTGAATTCCACCATTGTGCCATTATTCGAGAAGGTTCTGAGTGCTAGTGATGCTGGTCGAATTGGTCGTTTGGTCCTCCCAAAAGCATGTGCTGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattcatcaccagtttcccttgatgttatcattacagtttgaagtctactatagTGCCATTGTTTGAGAAGGTATTGAGTGCCAGTGATGCAGGTCGAATTGGTCGACTTGTTCTCCCAAAATCTTGTGCTGAG
ccttgat putative branch site (score: 5)
ttatcatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcataggttttgcctgttacacatcgtctatgttatatataaatttgattcatcaccagtttcccttgatgttatcattacagtttgaagtctactatagTGCCATTGTTTGAGAAGGTATTGAGTGCCAGTGATGCAGGTCGAATTGGTCGACTTGTTCTCCCAAAATCTTGTGCTGAG
- - - -ttttgcc
- - - - - - - - - - - - -gtctatg
- - - - - - - - - - - - - - - - - - - - - - - - - -atcacca