Sequence
atgc intronic sequence ATGC exonic sequencegtaagctatgacaccgaatctactattttttcgttaattaagttagtggtcgggactcgggatcaccttgtagatttagaagtttggtttcttagcaacttgtatttgagttctgcttttccactgtttttacatgtggaatatgcgactgataatcttgagatacctgcagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAACCTGTACGGTGACATTATTAGCGATCTGTGTGCCGGATTGGTTGGAGGACTAGGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03290.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 6
gtaagctat------gacaccgaatctactattttttc----gttaa--ttaagttagtggtcg----ggactcgggatcaccttgtagatttagaagtttggtttcttagcaacttgtatttgagttctgcttttccactgttttt-acatgtggaatatgcgactgataatcttgagata-------cctgcagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAACCTGTACGGTGACATTATTAGCGATCTGTGTGCCGGATTGGTTGGAGGACTAGGAT
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gtatgttgttctgctgataccaaaacctgtgctttgtttggtgttaatgttgaagcattcttcacactggtctgatgatctctgatcgacctgagaaatgcaaattatc--ctatttgtattctagccac-ttctattgctgtcctggacagttaattaatgacaccattgatttgtgaacattgtccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTATGGTGATATTATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCT
upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 5
gtaagctatgaca-ccgaatctact-attttttcgttaattaagttagtggtcgggactcgggatcaccttgtagatttagaagtttggtttcttagcaacttgtatttgagttctgcttttccactgtttttacatgtggaatatgcgactgataatcttgagatacctgcagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAACCTGTACGGTGACATTATTAGCGATCTGTGTGCCGGATTGGTTGGAGGACTAGGAT
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gtatgttctctcagctgaaagtattcatttttctgtcaattgttgttgtgctc----ttagtgatggcctgcctgaagcatcaggcagtgctaatatcaatt---atttttcttactattataagctgtgctgatgc-tgatgtaactcattc-tgaactgcatttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTATGGTGACATCATTAGCGATCTATGTGCTGGTTTGATTGGGGGCTTGGGCC
upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 5
gtaagctatgacaccgaatctactattttttcgttaattaagttagtggtcgggactcgggatcaccttgtagatttagaagtttggtttcttagcaacttgtatttgagttctgcttttccactgtttttacatgtggaatatgcgactgataatcttgagatacctgcagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAACCTGTACGGTGACATTATTAGCGATCTGTGTGCCGGATTGGTTGGAGGACTAGGAT
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--------------------------------gtatgttctgtcagttgaaagtatccg---tttctctgtcaattgttga---taggctcttgatagtt---atttttcttaatattatcagcttttctgatac--------tgttgtttatgaactgcatctgccttcagCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCC
upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 4
gtaagctatgacaccgaatctactattttttcgttaattaagttagtggtcgggactcgggatcaccttgtag-atttagaagtttggtttcttagcaacttgtatttgagttctgcttttccactgtttttacatgtggaatatgcgactgataatcttgagatacctgcagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAACCTGTACGGTGACATTATTAGCGATCTGTGTGCCGGATTGGTTGGAGGACTAGGAT
||| ||| | ||| | | | || || || ||||| | ||| || ||| | | | || | || | ||| | || |||||||||||| || || |||||||| ||||| | |||||||| ||||| || ||||| |||||||| || || ||||| || |||||||| ||| | || |
---------------------------------------------------------------------gtaatattggtgaacttgatgtatgagaaaactgcatttggaaa-tactta------gtatttggaaattaatgatattggttatttttctgaccttcc-gcagCTTGTGAAGAATCCTGCACTTTTCGATGTACTAGTGATGCCTAACCTTTATGGTGATATTATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTT
upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 4
gtaagctatgacaccgaatctactattttttcgttaattaagttagtggtcgggactcgggatcaccttgtagatttagaagtttggtttcttagcaacttgtatttgagttctgcttttccactgtttttacatgtggaat-atgcgactgataatcttgagatacctgcagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAACCTGTACGGTGACATTATTAGCGATCTGTGTGCCGGATTGGTTGGAGGACTAGGAT
| || | || | | || | | | | || ||| ||| | | | |||| | | | |||||| | ||||||||||| || || || ||||||||||| ||||||||||| ||||| || |||||||||||||| ||||| ||||| || ||| |||| |||||||| |
----------------------------------------------------------------gcaaaatatgtaagaaaaacgagatcattctaggcatatgatacagaaatgc------actaggataaaactaggaaccactctaacttctctcttgaataa---acagCTTGTGAAGAATCCTGCGCTTTTTGATGTGTTGGTGATGCCTAACCTCTATGGTGACATTATTAGTGATCTCTGTGCTGGCTTGATTGGGGGACTAGGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttccactgtttttacatgtggaatatgcgactgataatcttgagatacctgcagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAACCTGTACGGTGACATTATTAGCGATCTGTGTGCCGGATTGGTTGGAGGACTAGGAT
gactgat putative branch site (score: 3)
tttttacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctatgacaccgaatctactattttttcgttaattaagttagtggtcgggactcgggatcaccttgtagatttagaagtttggtttcttagcaacttgtatttgagttctgcttttccactgtttttacatgtggaatatgcgactgataatcttgagatacctgcagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAACCTGTACGGTGACATTATTAGCGATCTGTGTGCCGGATTGGTTGGAGGACTAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA