Sequence
atgc intronic sequence ATGC exonic sequencegtttgtatcgagaccaaatcaaaccttcccaaatacttgaaatttggttggtctaacctctcatgcaatgcaacagGTCAAAACCAAGGGAGGAACGAGTTTGTTATACGCTTGCAGCCTTCAGAGGCCATGTACATGAAGCTAACT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G27300.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G031107_T02 (Zea mays), 3'ss of exon 12
-----------------gtttgtatcgagaccaaatcaaaccttcccaaatacttg-------aaatttggttggtctaacctctcatgcaatgc--aacagGTCAAAACCAAGGGAGGAACGAGTTTGTTATACGCTTGCAGCCTTCAGAGGCCATGTACATGAAGCTAACT
| || | | | | || || | | | | ||||| | | || ||| | ||| | | ||| | || ||||| ||||| |||||||| |||||| ||||||| ||||| |||||||||||||| |||||
tgattactaccttcaatgattctgttcaaagca--ccagatttccatttaaacttgtctggttgcactgaacgtgtttaatcctctgtgctctcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAGCCATGTACATGAAACTAACG
upper sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G130230_T02 (Zea mays), 3'ss of exon 12
------------------gtttgtatcgagaccaaatcaaaccttcccaaatacttgaaatttgg----ttggtctaacctctcatgcaatgcaac--agGTCAAAACCAAGGGAGGAACGAGTTTGTTATACGCTTGCAGCCTTCAGAGGCCATGTACATGAAGCTAACT
|||| | | | | | || || | | || || | ||| |||| || || | ||| | || ||||| || || ||||||||||||||| | || || ||||| |||||||||||||| ||||||
aacgaatattttatattggtttattatgttgctctgttatgtctgaataagaattagatatcctggtatttgaactaaatataaatataacctgatgaagGCAAGAAGCAAGGAAGAAATGAGTTTGTTATACGCCTCCAACCATCAGAAGCCATGTACATGAAACTAACT
upper sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 12
---------------------gtttgtatcgagaccaaat-caaaccttcccaaatacttgaaatttggttgg-tctaacctctcatgcaatgcaa--cagGTCAAAACCAAGGGAGGAACGAGTTTGTTATACGCTTGCAGCCTTCAGAGGCCATGTACATGAAGCTAACT
|| | | || ||| | | | | ||||| | | | || || || || | | | | ||||||||| || ||||| || ||||||||||||||| |||| |||||||| || |||||||||||||| ||
tattagctagagtgtatgtttccttatcttgatggcaagtgcctattaatctaaata-tcaacttatgtttaaaccttactgtaaacttattcctgtttagGTCAAAAGCAGGGGAGAAATGAGTTTGTTATACGCCTGCAACCTTCAGAAGCTATGTACATGAAGCTTACA
upper sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ21593 (Selaginella moellendorffii), 3'ss of exon 11
gtttgtatcgagaccaaatcaaaccttcccaaatacttgaaatttggttggtctaacctctcatgcaatgcaacagGTCAAAACCAAGGGAGGAACGAGTTTGTTATACGCTTGCAGCCTTCAGAGGCCATGTACATGAAGCTAACT
| || | | | | || | | | || | || ||||| |||| || || | ||||||||||| || || ||||| |||||||| |||||||| |||||||| ||
------------gtaagctctgatccctgacactgtttttattcactcaaagacgatacttcgtttaaatatacagGCAAAAAACAGGGACGAAACGAGTTTGTCATGCGATTGCAACCTTCAGAAGCCATGTATATGAAGCTGACG
upper sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ23968 (Selaginella moellendorffii), 3'ss of exon 11
gtttgtatcgagaccaaatcaaaccttcccaaatacttgaaatttggttggtctaacctctcatgcaatgcaacagGTCAAAACCAAGGGAGGAACGAGTTTGTTATACGCTTGCAGCCTTCAGAGGCCATGTACATGAAGCTAACT
| | ||| | | || | | | || | || ||||| |||| || || | ||||||||||| || || ||||| |||||||| |||||||| |||||||| ||
------------gtaagctttgacccctgacactgtttttattcactcaaagacgatacttcgtttaaatatacagGCAAAAAACAGGGACGAAACGAGTTTGTCATGCGATTGCAACCTTCAGAAGCCATGTATATGAAGCTGACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaccttcccaaatacttgaaatttggttggtctaacctctcatgcaatgcaacagGTCAAAACCAAGGGAGGAACGAGTTTGTTATACGCTTGCAGCCTTCAGAGGCCATGTACATGAAGCTAACT
gtctaac putative branch site (score: 2)
aaatacttgaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtatcgagaccaaatcaaaccttcccaaatacttgaaatttggttggtctaacctctcatgcaatgcaacagGTCAAAACCAAGGGAGGAACGAGTTTGTTATACGCTTGCAGCCTTCAGAGGCCATGTACATGAAGCTAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC