Sequence
atgc intronic sequence ATGC exonic sequencegtctaaaatatttacttattcttatcctccaaaccatcacatttgctttggatagtgatctgtttctttccaatatcaatacattttcaaactttgtttcatccgctcagGTGTGCTGGGAGAAGTTTGCAAGGTACTTTGAGGTAGAGCTCAAAGAGGTGAAACTAAGTGAAGACTACTATGTTATGGATCCAGCTAAAGCTGTAGAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G17760.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G17760.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G101069_T01 (Zea mays), 3'ss of exon 3
gtctaaaatatttacttattcttatcctccaaaccatcacatttgctttggatagtgatctgtttctttccaatatcaatacattttcaaactttgtttcatccgctcagGTGTGCTGGGAGAAGTTTGCAAGGTACTTTGAGGTAGAGCTCAAAGAGGTGAAACTAAGTGAAGACTACTATGTTATGGATCCAGCTAAAGCTGTAGAGA
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-----------------gtacgtccggtccattgcgtgcaaaacg-tctgtctactggccatgggccatgcgatgccacga-gctgctgaaccaccaaacgcgcatgcagGTGTGCTGGGAGAAGTTCGCCAGGTACTTCGAGGTGGAGCTCAAGGAGGTGAAGCTCAAGGAAGGGTACTACGTGATGGACCCAGAGAAGGCCGCGGAGA
upper sequence: AT3G17760.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G34450.1 (Glycine max), 3'ss of exon 3
gtctaaaatatttacttattcttatcctccaaaccatcacatttgctttggatagtgatctgtttctttccaatatcaatacattttcaaactttgtttcatccgctcagGTGTGCTGGGAGAAGTTTGCAAGGTACTTTGAGGTAGAGCTCAAAGAGGTGAAACTAAGTGAAGACTACTATGTTATGGATCCAGCTAAAGCTGTAGAGA
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------accacgtaccagtacccatacc---aagtatt-tggtaactatgtgccagattttggggcctttagacctcaatgtttgatgttctttgaaattttcttcacagGTTTGTTGGGAAAAATTTGCAAGGTACTTTGAGGTAGAGCTCAAGGAAGTGAAACTCAAAGAAGGATACTATGTGATGGACCCTGCGAAAGCAGTTGAAA
upper sequence: AT3G17760.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G29900.1 (Glycine max), 3'ss of exon 3
gtctaaaatatttacttattcttatcctccaaaccatcacatttgctttggatagtgatctgtttctttccaatatcaatacattttcaaactttgtttcatccgct-cagGTGTGCTGGGAGAAGTTTGCAAGGTACTTTGAGGTAGAGCTCAAAGAGGTGAAACTAAGTGAAGACTACTATGTTATGGATCCAGCTAAAGCTGTAGAGA
||| || | | | | | | | |||| || | || | || || || | | || | | ||| |||| | | || | ||||| || ||||| || ||||||||||||||||||||||||||||| || |||||||| | || | |||||||| ||||| || || |||||||| || |
---taatgtaaaaagtgacgaattgcgt---agccataccaagtattt--ggtaactatgtgccagactttggggcctttagacct-caatgtttgat--gttcgttgcagGTTTGTTGGGAAAAATTTGCAAGGTACTTTGAGGTAGAGCTCAAGGAAGTGAAACTCAAAGAGGGATACTATGTGATGGACCCTGCGAAAGCTGTTGAAA
upper sequence: AT3G17760.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S34_308V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------gtctaaaatatttacttattcttatcctccaaaccatcacatt-tgctttggat--agtgatctgtttctttccaatatcaatacattttcaaactt--tgtttcatccgctcagGTGTGCTGGGAGAAGTTTGCAAGGTACTTTGAGGTAGAGCTCAAAGAGGTGAAACTAAGTGAAGACTACTATGTTATGGATCCAGCTAAAGCTGTAGAGA
||||| | | ||| || ||| || | | | || || || | | ||| || | || ||| || || ||| | ||| | | ||||||| ||||||||||| ||||| ||||| || || |||||| |||||| | || | ||||||||||| |||||||||||| | ||| || ||
gtacattttccaaacctatctctaagggaaa-aattaaaaaaattaaaaaaatcaacggacagcgattaagaccaaggaaaccctttgttgttattagaaattcacttacaatatcagcgttcggtttgtgtagGTGTGTTGGGAGAAGTTCGCAAGATACTTCGAAGTGGAGCTCCGAGAGGTAACTCTCAAAGAAGACTACTACGTTATGGATCCACACAGAGCAGTCGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatctgtttctttccaatatcaatacattttcaaactttgtttcatccgctcagGTGTGCTGGGAGAAGTTTGCAAGGTACTTTGAGGTAGAGCTCAAAGAGGTGAAACTAAGTGAAGACTACTATGTTATGGATCCAGCTAAAGCTGTAGAGA
tttcatcc CT-rich tract
aatatcaatacatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctaaaatatttacttattcttatcctccaaaccatcacatttgctttggatagtgatctgtttctttccaatatcaatacattttcaaactttgtttcatccgctcagGTGTGCTGGGAGAAGTTTGCAAGGTACTTTGAGGTAGAGCTCAAAGAGGTGAAACTAAGTGAAGACTACTATGTTATGGATCCAGCTAAAGCTGTAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG