Sequence
atgc intronic sequence ATGC exonic sequencegtaactatcaaaaaatctctttcctactcttgaaacattgtgaaatatttcactgccttacaacgtgaaaatatcttcattggttatagGAACTCAGCATCAAAAGTATATCCTGCCATGTATATAGAAAATGTTACTGAACTTGCATTTGATGATATTACACCTGAAGATCCTGATTTTCCATTCATT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G52410.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G52410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g64400.4 (Oryza sativa), 3'ss of exon 4
------gtaactatcaaaaaatctctttcctactcttgaa--------acattgtgaaatatttcactgccttacaacgtgaaaatatcttcattggttatagGAACTCAGCATCAAAAGTATATCCTGCCATGTATATAGAAAATGTTACTGAACTTGCATTTGATGATATTACACCTGAAGATCCTGATTTTCCATTCATT
| | | | | | | || | ||||| || | || | ||| || | || | | || || | || ||||||||| | | || ||||| ||||| || |||||||| || ||||| ||||||||||| ||||||||||| |||||||||||| |||||||||||| ||
caaaggatggaatttcatatttttgccttataattttgaatttggttcacttagtaattcattccatagactaagttcttgtttggatttcca---actatagGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGAACTTGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATA
upper sequence: AT5G52410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G077222_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------------------------------------------gtaactatcaaaaaatctctttcctactcttgaaacattg--tgaaatatttcactgccttacaacgtgaa--aa--tatcttcattggtt----atagGAACTCAGCATCAAAAGTATATCCTGCCATGTATATAGAAAATGTTACTGAACTTGCATTTGATGATATTACACCTGAAGATCCTGATTTTCCATTCATT
|| | || | || | || || || | | | | | | ||| || || || ||| || | | || | |||||| | |||||||| ||||| || |||||||| || ||||| ||||||||||||||||| ||| | |||||||||||||||||||||||||||||
gtgcatatctattattcctttgtatcagtagacctcccaagtgtttgttgcaaatatgcagtatggtcccatttctcttttgtcctatttcatattcttcatacgtttaaggtcattgcctcttgctgttaaattttcagttttgctctcttaggtgattattctgttaaccaacttattctcgtggtttccatacagGAACACTTTCTCAAAAGTGTATCCAGCAATGTATATTGATAATGTCACTGAACTTGCATTTGACGATGTCACACCTGAAGATCCTGATTTTCCATTCATA
upper sequence: AT5G52410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G140874_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------------------------gtaactatcaaaaaatctctttcctactcttgaaacattg--tgaaatatttcactgccttacaacgtgaaaa----tatcttcattggtt----atagGAACTCAGCATCAAAAGTATATCCTGCCATGTATATAGAAAATGTTACTGAACTTGCATTTGATGATATTACACCTGAAGATCCTGATTTTCCATTCATT
|| | || | || | || | || | | | | | | ||| || || ||| || | | || | |||||| | |||||||| |||| || |||||||| || ||||| ||||||||||||||||| ||| | |||||||||||||||||||||||||||||
gtgcatatctattattcctttgtatcagtagacctcccaagtgtttgttgcaaatatgcagtatggtcccatttctcttttgtcatatttcatattcttcatacgtttaaggtcattgcctcttgctgtcaaattttcagttttgctctcttaggtgattattctgttaaccaccttattctcgtggtttccatacagGAACACTTTCTCAAAAGTGTATCTAGCAATGTATATTGATAATGTCACTGAACTTGCATTTGACGATGTCACACCTGAAGATCCTGATTTTCCATTCATA
upper sequence: AT5G52410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G30160.1 (Glycine max), 3'ss of exon 4
gtaactatcaaaaaatctctttcctactcttgaa----acattgtgaaatat-ttcactgccttacaacgtgaaaatatcttcattggtta--tagGAACTCAGCATCAAAAGTATATCCTGCCATGTATATAGAAAATGTTACTGAACTTGCATTTGATGATATTACACCTGAAGATCCTGATTTTCCATTCATT
||| || | ||| | |||| | | |||| | || | | | | || | | | | | ||||| | ||| |||||||| |||||||||||||||||||| |||| |||||| ||||||||||||||| | || || || || ||||||||| | | ||||
gtagtaatttgtttctaccttctgcatatgtgaataacaaaatgtgttacatgtgtaatatttggcattacgtgtgcctttctggtaacttgttagGAGCACAGTTTCAAAAGTGTATCCTGCCATGTATATAGACAATGCTACTGAGCTTGCATTTGATGATGTCACTCCCGAGGACCCTGATTTTTCTTCCATT
upper sequence: AT5G52410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G25200.1 (Glycine max), 3'ss of exon 8
gtaactatcaaaaaatctctttcctactcttgaaacattgtgaaatatttcac-tgccttacaacgtgaaaatatcttcattggttatagGAACTCAGCATCAAAAGTATATCCTGCCATGTATATAGAAAATGTTACTGAACTTGCATTTGATGATATTACACCTGAAGATCCTGATTTTCCATTCATT
||| || | | | | | | ||| | || | |||| | | | | || || | | ||| | ||||| | ||| |||||||| |||||||||||||| ||||| ||||||||||| ||||||||||||||| | | || || || ||||||||| | | ||||
gtagtaatttatttctacatatgtgaataacaaaatgt-gttacatatgtaatatttggcattacatgtgactttctggtaacttgttagGAGCACAGTTTCAAAAGTGTATCCTGCCATGTACATAGACAATGTTACTGAGCTTGCATTTGATGATGTCATCCCCGAGGACCCTGATTTTTCTTCCATT
upper sequence: AT5G52410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G37850.1 (Glycine max), 3'ss of exon 7
-----------------------gtaactatcaaaaaatctctttcctactcttgaaacattgtgaaatatttcactgccttacaacgtgaaaatat-----cttcattggtta------tagGAACTCAGCATCAAAAGTATATCCTGCCATGTATATAGAAAATGTTACTGAACTTGCATTTGATGATATTACACCTGAAGATCCTGATTTTCCATTCATT
| ||||| | | | || ||| ||| | || || | | || | ||| |||| | | || ||| |||||| | ||||| |||||||||||||||| |||| | ||||||||| ||||||||||||||||| || ||||| || ||||||||| | ||||||
gtagttgtttatttcttctttctatcactattatgtgaaataacaa-tatataaaaaaggttg-gctattttctattattgtaatatgtggtgatatgtgtgcctttctgattacctttttagGAAAACTATCTCAAAGGTATATCCTGCCATGTTCGTAGACAGTGTTACTGAGCTTGCATTTGATGATATCACCCCTGAGGACCCTGATTTTTCTTTCATT
upper sequence: AT5G52410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G29970.1 (Glycine max), 3'ss of exon 3
-----------------------gtaactatcaaaaaatctctttcctactcttgaaacattgtgaaatatttcactgccttacaacgtgaaaatatct-----tcattggtta------tagGAACTCAGCATCAAAAGTATATCCTGCCATGTATATAGAAAATGTTACTGAACTTGCATTTGATGATATTACACCTGAAGATCCTGATTTTCCATTCATT
| | || | | | | | | ||| || | || | | | || | ||| |||||| | || ||| |||||| || ||||| ||||||||||||| ||| ||||| |||||||||| | ||||||||||||||| || ||||| || ||||||||| | | || |
gtagttggttatttcttcttcctctgattactatgtgaaataa--caagatataaaaaagtttagctatttgctattattgtaatatgtggcgatatctgtgcctttctgattacctttttagGAAAACAATCTCAAAGGTATATCCTGCCACGTACATAGACAATGTTACTGGGCATGCATTTGATGATATCACCCCTGAGGACCCTGATTTTTCTTGCACT
upper sequence: AT5G52410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 5
---------gta-actatcaaaaaatctctttcctactcttgaaacattgtgaaatatttcactgccttacaacgtgaaaatatct--tcattggttatagGAACTCAGCATCAAAAGTATATCCTGCCATGTATATAGAAAATGTTACTGAACTTGCATTTGATGATATTACACCTGAAGATCCTGATTTTCCATTCATT
||| | | | |||| |||| || | || | | | | | | | ||| ||| |||| || |||||| ||| ||||| |||||||| || ||||| |||| |||| ||||||||||||||||||||||||||||||||||||| ||||||||| ||| ||||
ctgtagcttgtagagtgcatcagcatctgaaggctaccaacataaattcacattggatgttgataacatgtgat-taataatttctatccattccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT
upper sequence: AT5G52410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S335_17V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaactatcaaaaaatctctttcctactcttgaaac--attgtgaaa-----tatttcactgcctt-acaacgtgaaa----atatcttcattggttat--agGAACTCAGCATCAAAAGTATATCCTGCCATGTATATAGAAAATGTTACTGAACTTGCATTTGATGATATTACACCTGAAGATCCTGATTTTCCATTCATT
||| | || | | | || ||| || || || | | | || || | | | || | | || |||| | | |||| ||| || | |||||| |||||| ||||| |||||| | || |||||||| |||||||| ||||| ||||||||||| |||||||| |||
---acttttggaagttgtgctaattatatatgatgttaatcgtccaagtggacactcgattgttttgatgatgcataatgttacttttttgttggatgtgtagGAGCTCTGCCACTAAAGTACTTCCTGCAATGTACATAGAAGGGGAGACAGAACTTGCTTTTGATGACATTACGCCTGAAGATCCAGATTTTCCTGCTATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acattgtgaaatatttcactgccttacaacgtgaaaatatcttcattggttatagGAACTCAGCATCAAAAGTATATCCTGCCATGTATATAGAAAATGTTACTGAACTTGCATTTGATGATATTACACCTGAAGATCCTGATTTTCCATTCATT
gccttac putative branch site (score: 3)
tcttcatt putative PPT
aaaatatcttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactatcaaaaaatctctttcctactcttgaaacattgtgaaatatttcactgccttacaacgtgaaaatatcttcattggttatagGAACTCAGCATCAAAAGTATATCCTGCCATGTATATAGAAAATGTTACTGAACTTGCATTTGATGATATTACACCTGAAGATCCTGATTTTCCATTCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA