Sequence
atgc intronic sequence ATGC exonic sequence...gcttaaatttaaaacaattgaagtttacagttggtattagtaactatcagaaaattctggcaatttactatatccataacatcactcttgtttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
Basic information
species | Glycine max |
transcript | GLYMA08G27560.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
gcttaaatttaaaacaattgaagtttacagttggtattagtaactatcagaaaattc-tggcaatttactatatccataacatcactcttgtttatt-gcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| | | | || | | ||| | ||| | | || || ||| ||| | ||| | | || ||||| | | | | || |||||||||||||||||||| ||||||||||| |||||||| ||||| || ||||| || || ||||| || || ||||| || |||||||| || ||||
-atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttct-taacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 3
---gcttaaatttaaaacaattgaagtttacagttggtattagtaactat--cagaaaattctggcaatttactatatccataacatcactcttgtttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
|| | | || | ||| | | || ||| ||| |||||| |||| |||| | || | ||||| | | |||||||||||||||||||||| |||||||||||||||||||| ||||| || ||||| | |||||||| || || || || || || ||||| || ||||
taagcatcgtgatggcgttatgagaagttaaattatgttttaagtcttataccagaaatttctc----tttattg-attcttaacaagataaactctacttgcagTGACATGGAATGTGACCTGCACATACTCACAATTTCTTGCTCAGAAGACTCCAACCTGTTGTGTATCTCTCTCGTCATTTTACAATGACACAATTGTGAA
upper sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g30260.1 (Oryza sativa), 3'ss of exon 3
gcttaaatttaaaacaattgaagtttacagttggtattagtaactatcagaaaattctggcaatttactatatccataacatcactcttgtttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| | | | ||| | | ||||||| | || || | | | | || ||| |||||||||| |||||||||||||||||||| || || ||| | ||||||| | |||| |||||||||| ||||||||||| || || ||||| || | |||
--------------------------gtaagtcatttcagtgttttttgtct--ttctggcg--tcacaattatgacaccctttcttcctttttttgcagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA
upper sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g35460.1 (Oryza sativa), 3'ss of exon 3
gcttaaatttaaaaca---attgaagtttacagttggtattagtaac-tatcagaaaattctggcaatttactatatccataacatcactcttgtttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| | || |||| | || ||| | | | | ||| | | || | | | || | | || | | || | |||||||||||||||||| ||||||||||| |||||||| || ||||| ||| || || ||||| || || || || ||| | ||||| | ||||
-ataggacttgttgtttgttttgagttctatagtagaaaaaattcctatattcagtactactagtagtacttcttaacaaaaaggaaatctctattca---cagTGACATGGAATGTGATCTGCACATACTCCCAATTTCTTGCACAAAAGGTTCCATCCTGCTGTGTTTCTCTCTCGTCGTTCGACAATGACAAAACTGTTGA
upper sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g41310.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------gcttaaatttaaa---acaattgaagtttacag-ttggtattagtaactatcagaaaattctggcaatttactatatccataac-atcactcttgtttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| | | | | ||||| | |||| || | | || | | | | | | | ||| | || || ||| ||||||||||||||||||||| |||||||| ||||| || | || |||| | |||| | || || || || || || ||||| || ||||||||| | |||
gtaagatttttttctgaagtttccatgatcttagtatttgccgtgcaaagtagttcagggatgagcttacaatctattgcaacagattcagaattgttcttgtttcgatactgccttttcgtgcatcatcggtgaccgcttgatttcttttgtgcagTGACATGGAATGTGACTTGCACATATTCACAGATTGTCGCGCAAAGATCTCCGACGTGCTGCGTTTCGCTCTCGTCTTTTTACAATGATACCATAGTTAA
upper sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
gcttaaatttaaaacaattgaagtttacagttggtattagtaac--tatcagaaaattctggcaatttactatatccataacatcactcttgtttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| ||| | | | | || | | || ||| | | || | | | | | | ||||| || | || ||||||||||||||||||||| |||||||| || |||||||| ||||| || ||||| || || ||||| || || ||||| || |||||||| || ||||
-ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacag-acattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G826714_T01 (Zea mays), 3'ss of exon 3
gcttaaatttaaaacaattgaagtttacagttggtattagt--aactatcagaaaattctggcaatttactatatccataacatcactcttgtttat-tgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
||| | | | | || | | || ||| ||| | | | | | | | | ||||| || ||||| ||||||||||||||||||||| |||||||| || |||||||| ||||| || ||||| || || ||||| || || ||||| || |||||||| || ||||
---ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAA
upper sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G009154_T01 (Zea mays), 3'ss of exon 2
gcttaaatttaaaacaattgaagtttacagttggtattagtaac--tatcagaaaattctggcaatttactatatccataacatcactcttgtttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| ||| | | | | || | | || ||| | | | | | | | | | | || || || | || ||||||||||||||||||||| |||||||| || |||||||| ||||| || |||| || || ||||| || || ||||| || |||||||| || ||||
-ttctaatcacagatagtcttaggaaaatttccatacaagttgcagttttgtctatattttatagcattgagagttcttatcag-acattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCTGTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
gcttaaatttaaaacaattgaagtttacagttggtattagta--actatcagaaaattctggcaatttactatatccataacatcactcttgtttat-tgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
||| | | | | || | | || ||| ||| | | | | | | | | ||||| || ||||| ||||||||||||||||||||| |||||||| || |||||||| ||||| || ||||| || || ||||| || ||
---ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------
upper sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 3
gcttaaatttaaaaca-attga-agtttacagttggtattagtaa----ctatcagaaaattctggcaatttactatatccataacatcactcttgtttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| || ||| ||||| | | | | || || || ||| | | | | | |||| ||||| ||| | ||| || ||| |||||||| |||||||| || ||||| || |||||||| |||||||| || || || | |||||||||||| | ||||| ||||||||| | || | || |
--aggatggcaagacacattgacaatggataatttgtgttcttaatatgcatttaaagagttctcaagatttaactaatcta----atcttcctgtcctatggcagTGACTTGGAATGTTACTTGCACGTATTCACAATTCCTGGCTCAGAAGACGCCTACATGTTGTGTCTCATTGTCATCGTTCTATAATAACACTATAGTATC
upper sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
---gcttaaatttaaaacaattgaagtttacagttggtattagtaactatcagaaaattctggcaatt-tactatatccataacatcactcttgtttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| | | | | || | | ||| | || | || | | || | | | || | |||| | ||| | | | | | | | |||||||||||||||| |||||||| || |||||||| ||| |||| ||||| ||| |||| |||||||| || ||||||||||| ||||| || |||| ||
agggagtgattcttaa--aggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgtactgggcc--taaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|151412694|gb|EV282506.1|EV282506EST: ACCCACTAAATTCATTACTTCAGACAAAAGGAGAGTGACCCAAGCACTGA TGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTC
genomic: ACCCACTAAATTCATTACTTCAGACAAAAGGAGAGTGACCCAAGCACTGAgtaagttata ... tttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcagaaaattctggcaatttactatatccataacatcactcttgtttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
ccataac putative branch site (score: 3)
ctcttgttt putative PPT
aatttactatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttaaatttaaaacaattgaagtttacagttggtattagtaactatcagaaaattctggcaatttactatatccataacatcactcttgtttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
- - - - - aaaacaa
- - - - - - - - - - - - - - -gttggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttctggc