Sequence
atgc intronic sequence ATGC exonic sequencegtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G63800.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------gtaatttttttaatcttatta--tcttatcagtttattcttgattttgagc------tccgat---tttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
| | ||||| | || |||| || | |||| || | | | | || ||| || || | | ||||| || | |||| | |||| || | ||| ||| | ||||||||||| |||||||||||||||||| | || ||||| ||||| |||||||| || |||||| | || || | || |
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgt-----tgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 1
gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgat--tttttttctaatgtttgtttggcgatt---tgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
|| || | | | | || | ||||| | | ||| ||| |||| |||| | ||| | || || |||| | ||||||||||| |||||||||||||||||| | || ||||| ||||| ||||||||||| ||||| |||| || || || |
-----------------------------gtgaggattttgtggcgtgtttcggtgatttttctatgggatttcgatggggattccttgatctgcgtttctactggctgtt-gatgcctg----cagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G053764_T01 (Zea mays), 3'ss of exon 1
-----gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
| | |||| | | || || || | | ||| || || | || |||| | | || | |||| ||| || ||| ||| | | | || ||||||||||| |||||||||||||||||| | || ||||| ||||| || ||||| |||||||||| || || || |
gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtg--ttctgcttgctttttt--ttttgatctggccattcttgccggctttcttggttta--tcggcgtcg-----cagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
| | || || || | | ||| || || | || |||| | | || | |||| ||| || ||| ||| | | | || ||||||||||| |||||||||||||||||| | || ||||| ||||| || ||||| |||||||||| || || || |
------------------gtctgttttccaattctgcctgaccgtg--ttctgcttgctttttt--ttttgatctggccattcttgccggctttcttggttta--tcggcgtcg-----cagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
-----gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA--------------------
| | |||| | | || || || | | ||| || || | || |||| | | || | |||| ||| || ||| ||| | | | || ||||||||||| |||||||||||||||||| | || ||||| ||||| || ||||| |||||||||| || || || |
gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtg--ttctgcttgctttttt--ttttgatctggccattcttgccggctttcttggttta--tcggcgtcg-----cagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G150867_T01 (Zea mays), 3'ss of exon 1
gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatt--tgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
|| | | |||||||| | || ||| || |||| | || ||| | |||||| | ||||||||||| |||||||||||||| ||| | || ||||| ||||| ||||||||||| ||||| |||| || || || |
-------------------------------------gtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctg----cagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 1
gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatt--tgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
| || | | || | | |||||||| | || ||| || |||| | || ||| | |||||| | ||||||||||| |||||||||||||| ||| | || ||||| ||||| ||||||||||| ||||| |||| || || || |
-------------------------gtgaggattctggtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctg----cagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G053764_T02 (Zea mays), 3'ss of exon 1
gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
|||| | | || || || | | ||| || || | || |||| | | || | |||| ||| || ||| ||| | | | || ||||||||||| ||||||||||| |||||| | || ||||| ||||| || ||||| |||||||||| || || || |
-----------tctcttggtctgttttccaattctgcctgaccgtg--ttctgcttgctttttt--ttttgatctggccattcttgccggctttcttggttta--tcggcgtcg-----cagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G053764_T05 (Zea mays), 3'ss of exon 1
-----gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA--------------------
| | |||| | | || || || | | ||| || || | || |||| | | || | |||| ||| || ||| ||| | | | || ||||||||||| ||||||||||| |||||| | || ||||| ||||| || ||||| |||||||||| || || || |
gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtg--ttctgcttgctttttt--ttttgatctggccattcttgccggctttcttggttta--tcggcgtcg-----cagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G053764_T04 (Zea mays), 3'ss of exon 1
-----gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
| | |||| | | || || || | | ||| || || | || |||| | | || | |||| ||| || ||| ||| | | | || ||||||||||| ||||||||||| |||||| | || ||||| ||||| || ||||| |||||||||| || || || |
gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtg--ttctgcttgctttttt--ttttgatctggccattcttgccggctttcttggttta--tcggcgtcg-----cagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G37650.1 (Glycine max), 3'ss of exon 1
gtaatttttttaatcttattatc-ttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgat-ttttttgtgatgatttg-atgtgagagt--ttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
| | | ||||| | || | | |||| | ||||| | | |||| | ||| || | | || ||| | | | ||| ||| || || | | | |||||||||||||| ||||||||||||| |||||| ||||||||||||||||||||||| |||||| |||||||||||||
-----gtctgtgatcttttcggaattgtttttgtattttcgatttcataaagtgttcttttgtataaatttgttgtcttttttccatttggggtgtgttggattgacatggatcaggtcatcatcagGATGATGAGTGATTACAAGGTGGAGACGATCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
|| || |||| || || | || | ||| | ||||| | | |||| ||| || | | | || | | ||| ||| || | | |||||||||||||| ||||||||||||| | |||| ||||||||||||||||||||||| |||||| |||||||||||||
gtgatcttttccgaattttttttttgt------attttcgatttcagaaagtgttcttttgcataa-attgttgtctttttccatttggggtgcgttggattgacatggatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 1
gtaatttttttaatcttatt---atcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
| | | ||||| | || || | | |||| | ||||| | | |||| ||| || | | | || | | ||| ||| || | | |||||||||||||| ||||||||||||| | |||| ||||||||||||||||||||||| |||||| |||||||||||||
-----gtctgtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataa-attgttgtctttttccatttggggtgcgttggattgacatggatcagGTCATCAGGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaatttttttaatcttattatcttatcagt-ttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
||| | || | | | | |||||| || || | ||| ||| | | || || || || ||| ||||| | |||||||||||||||||||||||| |||||| | |||||||| ||| || |||| ||| || || |||||| || |
---------------ggattgtgttgtgattacttttcttg--ttcgaattggtgcggtttggggaatcggcaagttgttgttgtatctgacgattcaagaatg------tgtgattgggtagGATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ23672 (Selaginella moellendorffii), 3'ss of exon 1
---------gtaatttttttaatcttattatcttatcagtttattcttgattttgag----ctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
| | | ||| | | | ||| | | | || | ||| ||| || || | | | | || ||| | | || ||| || | | || | |||||||||||||||||||||||||||||| | || ||||| ||| | ||||| ||| || ||| |||||| || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggctatgaaaaacctctctttcttcgctttcttcctctctgctaattcattgcttcttctttttgct--tcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ34378 (Selaginella moellendorffii), 3'ss of exon 1
gtaatttttttaatcttattatcttatcagtttattcttgatttt------gagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
|| | | | || | || || || ||||| | | || ||| || || | | | | || ||| | | || ||| || | | || | |||||||||||||||||||||||||||||| | || ||||| ||| | ||||| ||| || ||| |||||| || |
gtgagtctcgcctcctctcgaattt--caattccttcttcgctctccagtggacctctctttcttcgctttcttcctctctgctaattcattgcttcttctttttgct--tcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
atttgat putative branch site (score: 5)
atttttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA