Sequence
atgc intronic sequence ATGC exonic sequencegtgagttttttttggtgtctttatatccttcctctgctttttagtacaagagagacagaaacagagcagctctgttttagactttctgaaactgtttttgtctgtgatgattaattaaaaagGATGTTGATGTGGGAAGATGGGTTTTGTGGTGGAGGAAGAAGTGAAGATCTTTGTCTGGAAACAGACATTGAAGGTCATGAAGAAGATCTTGTCAGAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53900.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 2
gtgagttttttttggtgtctttatatccttcctctgctttttagtacaagagagacagaaacagagcagctctgttttagactttctgaaactgtttttgtctgtgatgattaattaaaaagGATGTTGATGTGGGAAGATGGGTTTTGTGGTGGAGGAAGAAGTGAAGATCTTTGTCTGGAAACAGACATTGAAGGTCATGAAGAAGATCTTGTCAGAAAA---
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---------ttttgatctttaatcattgtacacttttttttttttaaggttttggtttgtggtatttatatttgttattgactt---gtatttgtttttttttggtttga----------agGATGTTGATGTGGGAAGATGGGTTTTGCCAAGGAAGGGGT--TCAGGATGTCTGGA-AGATATTGATGGAGAGGATCCTGTCAGAAAGGCCTTCAGCAAAATG
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G35490.2 (Glycine max), 3'ss of exon 1
gtgagttt--tttttggtgtctttatatccttcctctgctttttagtacaagagagacagaaacagagcagctctgttttagactttctgaaactgtttttgtctgtgatgattaattaaaaagGATGTTGATGTGGGAAGATGGGTTTTGTGGTGGAGGAAGAAGTGAAGATCTTTGTCTGGAAACAGACATTGAAGGTCATGAAGAAGATCTTGTCAGAAAA---
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-tagttttgatcctcggtgtgactattgtacacttttcttttttaagattttggtttgtggtatata-----tttgttgttgacgtg-------tgttttttttt-----------ttttgaagGATGTTGATGTGGGAAGATGGGTTTTGCCGAGGAAGAGGT--TCAGGATGTCTGGA-AGATATTGATGGAGAGGATCCTGTCAGAAAGGCCTTCAGCAAAATG
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 2
gtgagttttttttggtgtctttatatccttcctctgctttttagtacaagagagacagaaacagagcagctctgttttagactttctgaaactgtttttgtctgtgatgattaattaaaa--agGATGTTGATGTGGGAAGATGGGTTTTGTGGTGGAGGAAGAAGTGAAGATCTTTGTCTGGAAACAGACATTGAAGGTCATGA-AGAAGATCTTGTCAGAAAA--
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-------------------catggatccaaacac-gcacttaaagattttgtttttattgattta-tggttttggtt---attgcttggattggtgatttaatgtgttgttgattttggtgcagGATGTTGATGTGGGAAGATGGGTTTTGCCG---AGGAAGGGTTTCAGATTGTTTGGAAGAGATTGATGGAGAGGATCCTATCAGGAAATCTTTTAGCAAAATG
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G27400.1 (Glycine max), 3'ss of exon 2
gtgagttttttttggtgtctttatatccttcctctgctttttagtacaagagagacagaaacagagcagctctgttttagactttctgaaactgtttttgtctgtgatgattaattaaaaagGATGTTGATGTGGGAAGATGGGTTTTGTGGTGGAGGAAGAAGTGAAGATCTTTGTCTGGAAACAGACATTGAAGGTCATGA-AGAAGATCTTGTCAGAAAA--
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--ggatccaaacacgcacaaaaagattgtatttttatttattgatttatg------------------gttttggttattgcttggttgg--tgatttaatgtgttgttaattttggtgcagGATGTTGATGTGGGAAGATGGGTTTTGCCG---AGGAAGAGTTTCAGATTGTTTGGAAGAGATTGATGGAGAGGATCCTATCAGGAAATCTTTTAGCAAAATG
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 3'ss of exon 2
gtgagttttttttggtgtctttatatccttcctctgctttttagtacaagagagacagaaacagagcagctctgttttagactttctgaaactgtttttgtctgtgatgattaattaaaaagGATGTTGATGTGGGAAGATGGGTTTTGTGGTGGAGGAAGAAGTGAAGATCTTTGTCTGGAAACAGACATTGAAGGTCATGAAGAAGATCTTGTCAGAAAA---
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------------tggtaacaaaagatggatgctcagtgtattatgatttg-gtgttcttttgagtgatttcttgaattgagttttttg----tttttccccccct-----tttcttttgaagGATGTTGATGTGGGAAGATGGGTTTTGCCG---AGGCAGAGTTGGAGAGTGTCTGGAAGAGATTGATGGTGAAGATCCTGTCAGAAAAGCCTTCAGCAAAATGMapped 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|164086056|gb|ES098445.1|ES098445EST: AGATTGGTGATGAAAGTGGCAGCTT GATGTTGATGTGGGAAGATGGGTTTTGTGGTGGAGGAAGAAAGTGAAGATC
genomic: AGATTGGTGATGAAAGTGGCAGCTTgtgagttttt ... aattaaaaagGATGTTGATGTGGGAAGATGGGTTTTGTGGTGGAGGAAGAA-GTGAAGATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctctgttttagactttctgaaactgtttttgtctgtgatgattaattaaaaagGATGTTGATGTGGGAAGATGGGTTTTGTGGTGGAGGAAGAAGTGAAGATCTTTGTCTGGAAACAGACATTGAAGGTCATGAAGAAGATCTTGTCAGAAAA
gattaat putative branch site (score: 3)
tgatgattaattaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttttttttggtgtctttatatccttcctctgctttttagtacaagagagacagaaacagagcagctctgttttagactttctgaaactgtttttgtctgtgatgattaattaaaaagGATGTTGATGTGGGAAGATGGGTTTTGTGGTGGAGGAAGAAGTGAAGATCTTTGTCTGGAAACAGACATTGAAGGTCATGAAGAAGATCTTGTCAGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG