Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgaccgttctaatcgcggttttaggttggttcggtttatgtgttcaactaatctaaaactgaatgagatttgatttttgaggatgatgttttgagcagGATCTTGGTGGATCTCTTGGGAGAGATGCTGCTACAGGAAGAGGAGTGTTGTTTGCAACAGAAGCTTTACTCAACGAACATGGAAAGACCATATCTGGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03910.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 5
gtaagtgaccgttctaatcgcggttttaggttggttcggtttatgtgttcaactaatctaaaactgaatgagatttgatttttgaggatgatgttttgagc-agGATCTTGGTGGATCTCTTGGGAGAGATGCTGCTACAGGAAGAGGAGTGTTGTTTGCAACAGAAGCTTTACTCAACGAACATGGAAAGACCATATCTGGAC
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gtaagtaattgtttgtttca---tttcaa--tggcc--attgaagtgaa-atcaaatcatatgcttaatatatcattgccctt----atgttttttcaaactagGATCTTGGTGGATCTCTCGGTAGAGACGCGGCTACAGGACGAGGAGTCCTCTTTGCAACAGAGGCTTTGCTTAATGAGTATGGGAAGAGTGTATCTGGAC
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G28770.1 (Glycine max), 3'ss of exon 4
gtaagtgaccgttctaatcgcggttttaggttggttcggtttatgtgttcaactaatctaaaactgaatgagatttgatttttgaggatgatgttttgagc-agGATCTTGGTGGATCTCTTGGGAGAGATGCTGCTACAGGAAGAGGAGTGTTGTTTGCAACAGAAGCTTTACTCAACGAACATGGAAAGACCATATCTGGAC
|| ||| | ||| || ||| || | | | || || || | | || | | | ||| ||| | ||| | | ||||||||||||||||||| || ||||| || ||||||||| | ||||| | ||||||||||| ||||| || || || |||| |||| |||||||||
gtgagtaattgtttgtttctgtcatttcatttcaatggccattgaagtgaaatcaaatcata--tgcttcatacactattgcccctcatgttttttcaaactagGATCTTGGTGGATCTCTAGGTAGAGACGCGGCTACAGGACGGGGAGTCCTCTTTGCAACAGAGGCTTTGCTTAATGAGTATGGGAAGAGTGTATCTGGAC
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 5
gtaagtgaccgttctaatcgcggttttaggttg-gttcggtttatgtgttcaactaatctaaaactgaatgagatttgatttttgaggatg-atgttttgagcagGATCTTGGTGGATCTCTTGGGAGAGATGCTGCTACAGGAAGAGGAGTGTTGTTTGCAACAGAAGCTTTACTCAACGAACATGGAAAGACCATATCTGGAC
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---aacaagaatttcaaccaaaaataaagagcgtgttcagaaaaatttgttga-taacatatc-ctaaaccaattcccatatctaactttccatgttcaaacaagGAACTCGGTGGATCTCTAGGCAGAGATGCAGCTACAGGACGAGGAGTCCTCTTTGCAACTGAGGCTTTGCTTAAGGAGCATGGGATGAGTCTATCCGGAC
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtgaccgttctaatcgcggttttaggttggttcggtttatgtgttcaact---aatctaaaactgaatgagatttgatttttgaggatgatgttttgagcagGATCTTGGTGGATCTCTTGGGAGAGATGCTGCTACAGGAAGAGGAGTGTTGTTTGCAACAGAAGCTTTACTCAACGAACATGGAAAGACCATATCTGGAC
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---attctttggcata-tcctatattgaaatcaccatgatgtatattgctgccttggattctgtttgtttctataatctgacagtgataaat--tctttaaattagGATCTCGGTGGATCTCTGGGCAGAGATGCAGCTACAGGAAGGGGAGTACTCTTTGCAACAGAGGCCCTTCTTCATGAACATGGGAAGAGCATTGCCGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaactaatctaaaactgaatgagatttgatttttgaggatgatgttttgagcagGATCTTGGTGGATCTCTTGGGAGAGATGCTGCTACAGGAAGAGGAGTGTTGTTTGCAACAGAAGCTTTACTCAACGAACATGGAAAGACCATATCTGGAC
atttgattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgaccgttctaatcgcggttttaggttggttcggtttatgtgttcaactaatctaaaactgaatgagatttgatttttgaggatgatgttttgagcagGATCTTGGTGGATCTCTTGGGAGAGATGCTGCTACAGGAAGAGGAGTGTTGTTTGCAACAGAAGCTTTACTCAACGAACATGGAAAGACCATATCTGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA