Sequence
atgc intronic sequence ATGC exonic sequence...aatttggttgtggatgagcaggtttttaggcgccatcaagcagtacttatgtttatccttgttgaagaacagtgcttcaactcttttgattgtgtttcagCTGTCATGCTCCATTTTCATCAGTCTGGTGTCAAGATTTAGAGCTGGATTGAAGGCAGAAATTGGAGTTTTTTTCCCTATGATTGTTCTCAGGGTCCTAG
Basic information
species | Glycine max |
transcript | GLYMA03G02610.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 1
---aatttggttgtggatgagcaggtttttaggcgccatcaagcagtacttatgtttatccttgttgaagaacagtg---cttcaactcttttgattgtgtttcagCTGTCATGCTCCATTTTCATCAGTCTGGTGTCAA---GATTTAGAGCTGGATTGAAGGCAGAAATTGGAGTTTTTTTCCCTATGATTGTTCTC-AGGGTCCTAG-------------
|| | | ||| ||||| | | | | | | || | | | || | | || | |||| |||| || || || | || | ||| |||| ||| | |||| | ||| | | | | | | | | | | | || | | ||||||| | || || | || |
gtatgttaaatacctctttagctcctttttc--tttttttgaatataagggtggatccaccgtatcaagaaaaattagattttgtattcttctgatgaatttccatctctgctgaacagGTTT--TCAG-CTGATATCAAACAGTTTTTGTGTTTG-TCGTTGTTGAAGAACAGTGCTTCTACTCTTATGATTATCTTCCAGCTTTCTTGCTCTATTTTCATC
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------------aatttggttg--tggatgagcaggtttttaggcgccatcaagcagtacttatgtttatccttgttgaagaacagt-gcttcaactcttt-tgattgtgtttcagCTGTCATGCTCCA----TTTTCATCAGTCTGGTGT----CAAGATTTAGAGCTGGATTGAAGGCAGAAATTGGAGTTTTTTTCCCT--ATGATTGTTCTCAGGGTCCTAG----------------------------------
|| ||| | | | | || | | ||| | || || | ||| | | || | ||| |||| || | | ||| | || | ||| | || ||||| | | || | | | || || | |||| | || | | | || | | || || || ||
gtttgttttgtttatcttcttgcattattataacccacgttaggtagattaaactatcatatctctagattcagtcttttttccctcagctttcaacattctgcttgatagttgcttggacagaatgtaatttagcttttggtgtttcttctgaaaatttggcatcaactcattatggaacagGTTCTTAGGCGCCATC--AAGCAGTATCTGTGTCTCTCCTTGCTGAAGAACAGTGCTTCAAATCTTATGATCATTTTCCAGCTTTCCTGCTCGATTTTACTT
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------------------------------------------------aatttggttgtggatgagcaggtttttaggcgccatcaagcagtacttatgtttatccttgttgaagaacagtgcttcaactcttttgattgtgtttcagCTGTCATGCTCCATTTTCATCAGTCTGGTGTCAAGATTTAGAGCTGGATTGAAGGCAGAAATTGGAGTTTTTTTCCCTATGATTGTTCTCAGGGTCCTAG
|| || | |||| ||| || ||||| ||||| |||||||| || ||| |||| |||||||||||||| ||||| |||||| ||||||| || ||||| || ||||||||||||||
ctttaaatgtgctccttattgttagtttagaattatttttctattaatggagtcctcaaattttaatcatggtctcctggatatgctggtggtaacacagATTCTTAGGTGCCATTAAGCAGTATTTGTGTCTATCATTGTTGAAGAACAGCGCTTCGACTCTTATGATTGTTTTCCAGCTTTCTTGCTCCATTTTCATT------------------------------------------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttatgtttatccttgttgaagaacagtgcttcaactcttttgattgtgtttcagCTGTCATGCTCCATTTTCATCAGTCTGGTGTCAAGATTTAGAGCTGGATTGAAGGCAGAAATTGGAGTTTTTTTCCCTATGATTGTTCTCAGGGTCCTAG
ttttgat putative branch site (score: 4)
ttttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatttggttgtggatgagcaggtttttaggcgccatcaagcagtacttatgtttatccttgttgaagaacagtgcttcaactcttttgattgtgtttcagCTGTCATGCTCCATTTTCATCAGTCTGGTGTCAAGATTTAGAGCTGGATTGAAGGCAGAAATTGGAGTTTTTTTCCCTATGATTGTTCTCAGGGTCCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - -ggttgtg
- - - - - - - - - - - - - - - - ccatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttca