Sequence
atgc intronic sequence ATGC exonic sequence...gcttagtgagtaggagtgcttaaagtaattgcctagtagaatttggcgttggttagcttatgaaaattttccattatttgttcactatatctgtttacagGTCACGAGTATGGTCAAGAAAGGTGCACAAAAAATAACACTTAGTATTGGTGATGGAGCCAATGATGTTAGCATGATTCAAGCTGCTCATGTTGGGGTTG
Basic information
species | Glycine max |
transcript | GLYMA08G40530.1 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G40530.1 (Glycine max), 3'ss of exon 22
lower sequence: LOC_Os10g27220.1 (Oryza sativa), 3'ss of exon 6
--gcttagtgagtaggagtgcttaaagtaattgcctagtagaatttggcgttggttagc-ttatgaaaattttccattatttgttcactatatctgtt-tacagGTCACGAGTATGGTCAAGAAAGGTGCACAAAAAATAACACTTAGTATTGGTGATGGAGCCAATGATGTTAGCATGATTCAAGCTGCTCATGTTGGGGTTG
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cagcagtcttatctggtttg-ttatatttatttctt-gcataacttat--ttggttagtacaatgctgaactgtaaacagctgacacttgctcatgttgtgtagGTTGCTAGCTTAGTTAAGAAAGGTGCCCATAAGATAACTCTCAGTATTGGTGATGGTGCTAATGATGTGAGTATGATTCAAGCTGCTCATGTGGGGATTG
upper sequence: GLYMA08G40530.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G020553_T01 (Zea mays), 3'ss of exon 1
--gctta-gtgagtaggagtgcttaaagtaattgcctagtagaatttggcgttggttagcttatgaaaattttccattatttgttcactatatctgtttacagGTCACGAGTATGGTCAAGAAAGGTGCACAAAAAATAACACTTAGTATTGGTGATGGAGCCAATGATGTTAGCATGATTCAAGCTGCTCATGTTGGGGTTG
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aagcaaatgggggcaatagt-ctctgattgattgcatggtttcattgcacagtcttgtatacgtgaaaatataaaatgctgacatta--atgtgtatatgtagGTTACAAGCTTAGTTAGGAAGGGTGCTGAGAAAATAACTCTCAGCATTGGTGACGGTGCTAATGATGTGAGTATGATTCAAGCTGCTCATGTTGGGATTG
upper sequence: GLYMA08G40530.1 (Glycine max), 3'ss of exon 22
lower sequence: Vv00s0189g00030.t01 (Vitis vinifera), 3'ss of exon 21
gcttagtgagtaggagtgcttaaagtaattgcctagtag-aatttggcgttggttagcttatgaaaattttccattatttgttcactatatctgtttacagGTCACGAGTATGGTCAAGAAAGGTGCACAAAAAATAACACTTAGTATTGGTGATGGAGCCAATGATGTTAGCATGATTCAAGCTGCTCATGTTGGGGTTG
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---------gtaaga-tgttttattttgttgttttgaagcaacttggctgaagt---atcatgtcagctgaatattgagaaatcactattgttgtttgtagGTGACAAGCCTGGTCAAGAAAGGTGCACGGAAAATAACACTTAGTATTGGTGATGGTGCCAATGACGTCAGCATGATTCAAGCGGCTCATGTTGGCGTTG
upper sequence: GLYMA08G40530.1 (Glycine max), 3'ss of exon 22
lower sequence: PP1S87_152V6.1 (Physcomitrella patens), 3'ss of exon 22
gcttagtgagtaggagtgcttaaagtaattgcctagtagaatttggcgttggttagcttatgaaaattttccattatttgttcac-----tatatctgtttacagGTCACGAGTATGGTCAAGAAAGGTGCACAAAAAATAACACTTAGTATTGGTGATGGAGCCAATGATGTTAGCATGATTCAAGCTGCTCATGTTGGGGTTG
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--tttctgagtattcacacttttgaaaagtgtagttcaagttctagc-ttaggtatgttatgtaa--ttttcattattcgtttgcacttccatttttgtatgcagGTGACAACACTCATCAAGGACGATGCTAAGAAGATTACCTTGAGCATTGGTGATGGAGCCAATGATGTTAGTATGATTCAGGCTGCTCACATTGGAGTAG
upper sequence: GLYMA08G40530.1 (Glycine max), 3'ss of exon 22
lower sequence: EFJ31523 (Selaginella moellendorffii), 3'ss of exon 22
gcttagtgagtaggagtgcttaaagtaattgcctagtagaatttggcgttggttagcttatgaaaattttccattatttgttcactatatctgtttacagGTCACGAGTATGGTCAAGAAAGGTGCACAAAAAATAACACTTAGTATTGGTGATGGAGCCAATGATGTTAGCATGATTCAAGCTGCTCATGTTGGGGTTG
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-----------------------------------------------gtaagtgtttcctttccatttgtgtgtt-ttgatcttgtaattctattggcagGTAACGAAACTAGTGAAAGACGGAGCCAAGAAAATAACTTTAAGCATTGGTGATGGTGCTAACGACGTGAGCATGATTCAAGCTGCTCATATCGGGGTTGMapped 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|254336296|gb|GR842475.1|GR842475EST: ATTGTCACGCTGTAGTTTGCTGCCGAGTTTCTCCTTTACAGAAAGCACAG GTCACGAGTATGGTCAAGAAAGGTGCACAAAAAATAACACTTAGTATTGGT
genomic: ATTGTCACGCTGTAGTTTGCTGCCGAGTTTCTCCTTTACAGAAAGCACAGgtaaagctca ... ctgtttacagGTCACGAGTATGGTCAAGAAAGGTGCACAAAAAATAACACTTAGTATTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgttggttagcttatgaaaattttccattatttgttcactatatctgtttacagGTCACGAGTATGGTCAAGAAAGGTGCACAAAAAATAACACTTAGTATTGGTGATGGAGCCAATGATGTTAGCATGATTCAAGCTGCTCATGTTGGGGTTG
tctgttt CT-rich tract
ttatgaaaattttcca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttagtgagtaggagtgcttaaagtaattgcctagtagaatttggcgttggttagcttatgaaaattttccattatttgttcactatatctgtttacagGTCACGAGTATGGTCAAGAAAGGTGCACAAAAAATAACACTTAGTATTGGTGATGGAGCCAATGATGTTAGCATGATTCAAGCTGCTCATGTTGGGGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
-cttagtg
- - - - - - -gagtgct
- - - - - - - - - - - - - - ttgccta
- - - - - - - - - - - - - - - - - - - - - - - -gttggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttcac