Sequence
atgc intronic sequence ATGC exonic sequencegtttaactgaggggttttggtttctttacttttcttagtttttaggggtctattcaattttacattgtaaccggaattcttgtttttcttatccaatacagGATGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12170.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G129987_T01 (Zea mays), 3'ss of exon 2
gtttaactgaggggttttggtttctttacttttcttagtttttaggggtctattcaattt-tacattgtaaccggaattcttgtttttcttatccaatacagGATGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATG
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--------gtaggatctcaagcacaaagcatt----atttttt-----tccactcgtttagtgcaatgtatctcaaata--taatgttctgtgctac--cagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATTACTGATGATG
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G088440_T01 (Zea mays), 3'ss of exon 2
gtttaactgaggggttttggtttctttacttttcttagtttttaggggtctattcaattttacattgtaaccggaattcttgtttt-tcttatccaatac-agGATGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATG
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----------------gtagtatctcaaccata---aacttgaatgtttttctataggcatttagtgcaaa-gtatctcaaatataatgttatatgttgctagGAAACCAAAGAGAAGTTTCAGCTGTTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATG
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 2
gtttaactgaggggttttggtttctttacttttcttagtttttaggggtctattcaattttacattgtaaccggaattcttgtttt-tcttatccaatac-agGATGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATG
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----------------gtagtatctcaaccata---aacatgaatgtttttctacaggcatttagtgcaaa-gtatctcaaatataatgttatatgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATG
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G885923_T01 (Zea mays), 3'ss of exon 2
gtttaactgaggggttttggtttctttacttttcttagtttttaggggtctattcaattttacattgtaaccggaattcttgtttt-tcttatccaatac-agGATGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATG
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----------------gtagtatctcaaccata---aacatgaatgtttttctacaggcatttagtgcaaa-gtatctcaaatataatgttatatattgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTCGAGATGCAGAGAAAAGAGCTTTATAGGATATGACTGGCATCACTGATGATG
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G32480.1 (Glycine max), 3'ss of exon 2
gtttaactgaggggttttggtttctttacttttcttagtttttaggggtctattcaattttacattgtaaccgg-aattcttgtttttcttat-ccaatacagGATGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATG
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caaccttttatatctcctgaatatgccatcatggtcttttcactagaatatatt---ttaggtgttgacacttgtaattgattagtttcttgtgttgttgcagGAAGCTAAGGAGAAATTCCAGCAACTGCAAAAAGTGATATCGATTCTCGGGGATGAAGAGAAGCGAGCTCTCTATGATCAGACTGGTTGTGTTGATGATG
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 2
gtttaactgaggggttttggtttctttacttttcttagtttttaggggtctattc--aattttacattgtaaccggaattcttgtttttcttatccaatacagGATGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATG
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gtgcatttgatttctaatgatgccaaaa----tcctattctccatatatccgttgcaagggtggttttctggttgttaccctttgtttttttccctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCACTCTATGATCAGACTGGTTGTGTTGATGATGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|164094702|gb|ES014725.1|ES014725EST: GCATTGAGGCTTCATCCTGATAAAAACAAGGATGATGAG GATGCTAAAGAGAAATTTCAGCAGTTGCAAAA
genomic: GCATTGAGGCTTCATCCTGATAAAAACAAGGATGATGAGgtttaactga ... tccaatacagGATGCTAAAGAGAAATTTCAGCAGTTGCAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtctattcaattttacattgtaaccggaattcttgtttttcttatccaatacagGATGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATG
ttgtaac putative branch site (score: 2)
ttcttgtttttcttat putative PPT
attcaattttacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttaactgaggggttttggtttctttacttttcttagtttttaggggtctattcaattttacattgtaaccggaattcttgtttttcttatccaatacagGATGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG