Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttttctattgatttgtttatcctacaaatggttcaacttttaggttaactactatcttgaatcatgcagGTCCCATTTTTCTCTCAAATGGATGATCAGCTGCTTGATGCGATATGTGAGCGCCTGGTTTCTTCTCTGTGTACTGAAGGGACTTACCTTGTACGTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G30360.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G30360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G005791_T01 (Zea mays), 3'ss of exon 5
--------------gtaagtttttctattgatttgtttatcctacaaatgg--ttcaac----ttttaggttaactactatcttgaatca------tgcagGTCCCATTTTTCTCTCAAATGGATGATCAGCTGCTTGATGCGATATGTGAGCGCCTGGTTTCTTCTCTGTGTACTGAAGGGACTTACCTTGTACGTGAAG
| || || || | | ||| ||||| || | ||| || || | | ||| | ||| ||| ||||||| || |||||||| || |||||||||||||| |||||||| || |||||||| || || || || ||||| || |||| || ||| |||| ||||| |
atcctttgccccctgaaaaagattgcatcg-taaatttgaactacacattgctttctacataattgcatggtaaatctcgctttgtatcgcaatgttgcagGTTCCTTTTTTCTCCCAGATGGATGATCAGCTTCTTGATGCCATCTGTGAGCGTCTTGTATCATCACTGTGCACAAAAGGCACATACATTGTCCGTGAGG
upper sequence: AT4G30360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G436583_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------------------------------------------gtaagtttttc-tattgatttgtttatcctacaaatggttcaacttttag----gttaactact--atcttg--------aatcatgcagGTCCCATTTTTCTCTCAAATGGATGATCAGCTGCTTGATGCGATATGTGAGCGCCTGGTTTCTTCTCTGTGTACTGAAGGGACTTACCTTGTACGTGAAG
| ||| | | | | | || ||| ||| || | || |||| |||| ||||| ||| ||||||||||| ||||||| || ||||| |||||||| || || || ||||| ||||||||||| || || || | || || || || ||| |||| || ||||
gtaaatcagcttactacctttgctctctcgtttttttattggtcagcaacagagttagtaacttagtagtgctagttgaattcttatccatttgtgaggtgatcagtggcgcgcctctaacggctagtcttacgaataacctgaccatgagtagtgttacttacttaatcttttatatcgcaatgctgcagGTCCCACTTTTCTCCCAGATGGACGATCAGCTTCTAGACGCCATATGCGAGCGCCTGGTATCGTCCTTGAGCACAGAGGGCACATACATTGTCCGAGAAG
upper sequence: AT4G30360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G24950.1 (Glycine max), 3'ss of exon 6
-----------------------gtaagtttttctattgatttgttt---atcctacaaatggttcaacttttaggttaactactatcttgaatcatgcagGTCCCATTTTTCTCTCAAATGGATGATCAGCTGCTTGATGCGATATGTGAGCGCCTGGTTTCTTCTCTGTGTACTGAAGGGACTTACCTTGTACGTGAAG
| | | | | || | || || || | | || || | | | | | ||||| || || ||||| || |||||||||||||| || ||||| ||||||||||| ||||| || |||||| | ||| |||| || ||| |||| ||||| |
atgattgattcctattgatgccaatgaacacaaatgctagtaagtataaaatttactctattgtaagagtgtttaacaaattccctttctatgcttt-cagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG
upper sequence: AT4G30360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G30030.2 (Glycine max), 3'ss of exon 7
-------------------gtaagtttttctattgatt-tgtttatcctacaaatggttcaacttttag--gttaac---tactatcttgaatcatgcagGTCCCATTTTTCTCTCAAATGGATGATCAGCTGCTTGATGCGATATGTGAGCGCCTGGTTTCTTCTCTGTGTACTGAAGGGACTTACCTTGTACGTGAAG
| | | || || | | | || || | || | | | || ||||| | | | | | | ||||| || || ||||| || ||||||||||| || || ||||| ||||||||||| ||||| || |||||| | ||| |||| || ||| |||| ||||| |
aagattgattcccattgatgccaatgaacatagaaatgatagtaagtataaaatttactctattgtaagtatttaacaaattccctttctatggtttcagGTTCCCTTCTTCTCACAGATGGATGATCAACTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGAACCTACATTGTTCGTGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttatcctacaaatggttcaacttttaggttaactactatcttgaatcatgcagGTCCCATTTTTCTCTCAAATGGATGATCAGCTGCTTGATGCGATATGTGAGCGCCTGGTTTCTTCTCTGTGTACTGAAGGGACTTACCTTGTACGTGAAG
ggttaac putative branch site (score: 3)
aactttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttttctattgatttgtttatcctacaaatggttcaacttttaggttaactactatcttgaatcatgcagGTCCCATTTTTCTCTCAAATGGATGATCAGCTGCTTGATGCGATATGTGAGCGCCTGGTTTCTTCTCTGTGTACTGAAGGGACTTACCTTGTACGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG