Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttacatcactttgatttttatggatttaaagtagatttggttaaaggattttgataggagctagatttgaaaaatgcagGGTTGCTATGTTTGTATTGTCACTGGATACTGTGAAGGAGGAGACAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G44200.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 3
gtaagttttacatcactttgatttttatggatttaaagtagatttggttaaaggattttgataggagctagatttgaaaaatgcagGGTTGCTATGTTTGTATTGTCACTGGATACTGTGAAGGAGGAGACAT
||| | | || || | || || || | ||||| | | || | || | | | | |||||||||||||||||| || |||||||| || || |||||||| ||||| ||
-----gtttgtgg-attaggaacttactatatctagctta--tctggtttatacttatttagttgacatgggtc--agtaatgcagGGTTGCTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGATAT
upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 4
gtaagttttacatcactttgatttttatggatttaaagtagatttggttaaaggattttgataggagctagatttgaaaaatgcagGGTTGCTATGTTTGTATTGTCACTGGATACTGTGAAGGAGGAGACAT
||||| | | | || | | | | | || || || ||| | | | || | || ||||||||||| ||||| || |||||||| || || |||||||| ||||||||
----gttttgtagttcaggaacttgttcttaccttgtttct-tctgtttgaacttatttagttga--caaggt--gagttatgcagGGTTGTTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGACAT
upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 3
------------------------gtaagttttacatcactttgat---ttttatggatttaaagtagatttggttaaaggattttgataggagctagatttgaaaaatgcagGGTTGCTATGTTTGTATTGTCACTGGATACTGTGAAGGAGGAGACAT
|||| | ||| || || | || | || || | | | || || || || || | | | |||||||||||||||| || ||||||||||||||||||||||| ||||||||
gtgagagaccctttaagtttttgtgtaatgtaatcatagtcttaatagttactacagtattgaactctctgttgtaaactatttctgctaagcacattctacttctgttgcagGGTTGCTATGTCTGCATTGTCACTGGATACTGTGAAGGTGGAGACAT
upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 3
--------------------------------gtaagttttacatcactttgatttttatgg--atttaaagtagatttggtta-aaggattttgataggagctagatttga--------aaaatgcagGGTTGCTATGTTTGTATTGTCACTGGATACTGTGAAGGAGGAGACAT
| | | || | | | ||| | | | | ||| || | || || | |||| | ||| | || | || |||||||||||||||| ||||| ||||||||||||||||| ||||||||
gttagagaaagcacaccgtttcaattgttatattgcagtatgcagtaatgtactttctgctgtaaactggagtttgttggattgtaacgtttttctttttggctgtgtatgtttttggttgtattgtagGGTTGCTATGTTTGCATTGTTACTGGATACTGTGAAGGTGGAGACAT
upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G09910.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------gtaagttttacatcactttgattt---ttatggatttaaagta----gatttggttaaaggattttgataggagctagatttgaaaaatgcagGGTTGCTATGTTTGTATTGTCACTGGATACTGTGAAGGAGGAGACAT
||| ||||| | | || | || || | | |||| || | | ||| | | | ||| | |||||||||||||||| || |||||||| |||||||||||||| ||||||||
gtgaagacccttaaaatttttgtataatgtaatcatagacttagtttctttcagttaattgttaatagttacagtattgcaatctctgttgtgaactagaagtgtgagaataatgactgtttacttttctgctaagcacattctactgttgcagGGTTGCTATGTCTGCATTGTCACCGGATACTGTGAAGGTGGAGACAT
upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------gtaagttttac-atcactttgatttttatggatttaaagtagatttggtta--aaggattttgataggagctagatttgaaaaatgcagGGTTGCTATGTTTGTATTGTCACTGGATACTGTGAAGGAGGAGACAT
||| ||| | | | | |||| || || ||| || | | ||| ||| | | || || | | | || | || ||||||| |||||||| ||||| ||||||||||||||||| ||||||||
gtgagccaaagcattgcgtttcgattgttattttgcagtatgcagtgttgtacgttctcctgtaaacttgaattagttgtattgtaa-tggttttatttatttattacttaagtatgtttttggtt---gtattgtagGGTTGTTATGTTTGCATTGTTACTGGATACTGTGAAGGTGGAGACAT
upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 3
gtaagttttacatcactttgatttttatgga-----tttaaagtagatttggttaaaggattttgataggagcta-gatttgaaaaatgcagGGTTGCTATGTTTGTATTGTCACTGGATACTGTGAAGGAGGAGACAT
||| || | | | | ||||| || ||| ||| || | | | | ||||| | ||| | |||||||||||||||||||| |||||||||||||| |||||||||||||||||
gtaggtcctggaaattctagttttttgacgaatttttttgctgtaaatgcgacctt-gtactgaatcgagagctttgggttgga--atgcagGGTTGCTATGTTTGCATTGTCACTGGATATTGTGAAGGAGGAGACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaaagtagatttggttaaaggattttgataggagctagatttgaaaaatgcagGGTTGCTATGTTTGTATTGTCACTGGATACTGTGAAGGAGGAGACAT
ttttgat putative branch site (score: 4)
tagatttgaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttacatcactttgatttttatggatttaaagtagatttggttaaaggattttgataggagctagatttgaaaaatgcagGGTTGCTATGTTTGTATTGTCACTGGATACTGTGAAGGAGGAGACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA