Sequence
atgc intronic sequence ATGC exonic sequence...tgtgttatgattcttttttcttatatgctcacgttattgtctctcttttccttattctaaatttaaaactgaatcctgagtctgtctattgtttacacagGTGGTGGGAAAGGAGGGCCGGGTTTATCTGTAGAAGCTTTAGAGAAAATGATGGAAGATCCAACAGTCCAGAAGATGGTTTACCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G16620.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G16620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os04g35900.1 (Oryza sativa), 3'ss of exon 7
------tgtgttatgatt----cttttttcttatatgc-tcacgttattgtctctcttttccttattctaaatttaaaactgaatcctgagtctgtctattgtttac-----acagGTGGTGGGAAAGGAGGGCCGGGTTTATCTGTAGAAGCTTTAGAGAAAATGATGGAAGATCCAACAGTCCAGAAGATGGTTTACCC
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gtaagtactattatcattagcacatttttattattcacatttagtttttttatttgtgtttctgtttaaggatttttagttatctgctgttgataaatgtcctaaactgattatgtatgtagGCAATTCAGGGCCTATGTTGTCCGTTGATACAATTGAGAAAATGATGGAAGATCCAGCCGTGCAGAAGATGGTTTACCC
upper sequence: AT5G16620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G353213_T02 (Zea mays), 3'ss of exon 8
--------------------------------------tgtgttatgattcttttttcttatatgctcacgttattgtctctctttt-ccttattctaaatttaaaactgaatcctgagtctgtctattgtttacacagGTGGTGGGAAAGGAGGGCCGGGTTTATCTGTAGAAGCTTTAGAGAAAATGATGGAAGATCCAACAGTCCAGAAGATGGTTTACCC
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gtaagcaattgagcacacacacactgtggatctccttttgtattttagta--tctttcttataaaatcatttggtagtgttccttttatctggttttcctagttgatctaaat---agattcttcaactgattctattatagAT---AACTCGGCATCTATGCTATCCGTTGAGACAATTGAGAAAATGATGGAAGATCCAGCTGTGCAGAAGATGGTGTATCC
upper sequence: AT5G16620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: AC204045.3_FGT005 (Zea mays), 3'ss of exon 3
------------------------------tgtgttatgattc---ttttttcttatatgctcacgttattgtctctctttt-ccttattctaaatttaaaactgaatcctgagtctgtctattgtttacacagGTGGTGGGAAAGGAGGGCCGGGTTTATCTGTAGAAGCTTTAGAGAAAATGATGGAAGATCCAACAGTCCAGAAGATGGTTTACCC
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gtaagcaattgaacatacacattgcagatctctatttttgtctcagtatcttcttataaaatgatttggtagtgtaccttttatctagttttcatggttgatctgaat---agattcctcaactgattctgctatagGTC---AATCAGGACCTATGCTATCTGTTGAGACAATTGAGAAGATGATGGAAGATCCAGCTGTGCAGAAGATGGTTTATCC
upper sequence: AT5G16620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G053019_T01 (Zea mays), 3'ss of exon 7
------------------------------------tgtgttatgattcttttttcttatatgctcacgttattgtctctcttttccttattctaaatttaaaactgaatcctgagtctgtctattgtttacacagGTGGTGGGAAAGGAGGGCCGGGTTTATCTGTAGAAGCTTTAGAGAAAATGATGGAAGATCCAACAGTCCAGAAGATGGTTTACCC
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gtaagcaattgaacatacacattgcggatctctatttgtgtctcagtatcttcttataaaatgatt-tggtagtgtaccttttatctagttttcatggttgat-ctgaat--tgattcc-tcaactgattctgctatagGTC---AATCAGGACCTATGCTATCTGTTGAGACAATTGAGAAGATGATGGAAGATCCAGCTGTGCAGAAGATGGTTTATCC
upper sequence: AT5G16620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G05480.1 (Glycine max), 3'ss of exon 10
tgtgttatgattcttttttcttatatgctcacgttattgtctctcttttccttattctaaatttaaaactgaatcctgagtctgtctattgtttacacagGTGGTGGGAAAGGAGGGCCGGGTTTATCTGTAGAAGCTTTAGAGAAAATGATGGAAGATCCAACAGTCCAGAAGATGGTTTACCC
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-----tataggttttacaattattgttctttcaatgtttccttcaatgagctgcattatgggttaatcaaatgtcgtaaacatgcc-attatttattt------ttggatagAAAAATCAGTCTTGTCAGTGGATGCTTTGGAGAAAATGATGGAGGACCCAACAGTGCAGAAGATGGTTTATCC
upper sequence: AT5G16620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G31810.1 (Glycine max), 3'ss of exon 7
tgtgttatgattcttttttcttatatgctcacgttattgtctctcttttccttattctaaatttaaaactgaatcctgagtctgtctattgtttacacagGTGGTGGGAAAGGAGGGCCGGGTTTATCTGTAGAAGCTTTAGAGAAAATGATGGAAGATCCAACAGTCCAGAAGATGGTTTACCC
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-----tataggttttacaattattgttctttcaatgtttccttcaatgagctgcattatgggttaatcaaatatccttaacatgcc-attatttattt------ttggatagAAAAATCAGCCTTGTCAGTGGATGCTTTGGAGAAAATGATGGAGGACCCAACAGTGCAGAAGATGGTTTATCC
upper sequence: AT5G16620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 7
tgtgttatgattcttttttcttatatgctcacg-ttattgtctctcttttccttattctaa--atttaaaactgaatcctgagtctgtctattgtttacacagGTGGTGGGAAAGGAGGGCCGGGTTTATCTGTAGAAGCTTTAGAGAAAATGATGGAAGATCCAACAGTCCAGAAGATGGTTTACCC
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-atttaatcacagctaagaataatttaattttgcttgatgactctgtgtggttttttatgatggtttggtatt---tcctaaat-----tgttgaacattcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC
upper sequence: AT5G16620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S159_2V6.1 (Physcomitrella patens), 3'ss of exon 7
-------tgtgttatgattcttttttcttatatgctcacgttattgtctctcttttccttattctaaatttaaaactgaatcctgagtc--tgtctattgtttacacagGTGGTGGGAAAGGAGGGC---CGGGTTTATCTGTAGAAGCTTTAGAGAAAATGATGGAAGATCCAACAGTCCAGAAGATGGTTTACCC
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accttaaattgggaaagagggtttaaattatttacttagagtagttcattttctattgggagaatttcgtaatgattgggttgtttgttgttgtctctagCATGGAATTCTGCTGGAAAAGGAAAACAGACGGTCTTCACTGTTGACCAATTGGAGAAGATGATGGAGGATCCAACAGTTCAAAAGATGGTTTACCCMapped 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|164167802|gb|ES048922.1|ES048922EST: AGCTGGTCCGGCAAATGGTGCCACTGCTTCAGAGGTTTTTCAATCTTTGG GTGGTGGGAAAGGAGGGCCGGGTTTATCTGTAGAAGC
genomic: AGCTGGTCCGGCAAATGGTGCCACTGCTTCAGAGGTTTTTCAATCTTTGGgtgagttatt ... gtttacacagGTGGTGGGAAAGGAGGGCCGGGTTTATCTGTAGAAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttccttattctaaatttaaaactgaatcctgagtctgtctattgtttacacagGTGGTGGGAAAGGAGGGCCGGGTTTATCTGTAGAAGCTTTAGAGAAAATGATGGAAGATCCAACAGTCCAGAAGATGGTTTACCC
ttctaaa putative branch site (score: 2)
ttattctaaatttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgttatgattcttttttcttatatgctcacgttattgtctctcttttccttattctaaatttaaaactgaatcctgagtctgtctattgtttacacagGTGGTGGGAAAGGAGGGCCGGGTTTATCTGTAGAAGCTTTAGAGAAAATGATGGAAGATCCAACAGTCCAGAAGATGGTTTACCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaatc