Sequence
atgc intronic sequence ATGC exonic sequence...agcatattgagttttgcttcatttatgtggaatttgtatatataaggtcagggttacatattttattttgatgcaatgatggttgttacaaaattcacagGTGGTCACTTGGAGCTATTATGTACGAAATGCTGGTGGGATATCCTCCTTTTTATTCTGATGATCCAATGTTAACATGCAGGAAG
Basic information
species | Glycine max |
transcript | GLYMA10G04410.3 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
agcatattgagttttgcttcatttatgtggaatttgtatatataaggtcagggttacatattttattttgatgcaatgatggttgttacaaaattcacagGTGGTCACTTGGAGCTATTATGTACGAAATGCTGGTGGGATATCCTCCTTTTTATTCTGATGATCCAATGTTAACATGCAGGAAG
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-----------gtaagcatcgtttacataaatatctcgtgccatggacc-----tcttgagtttgcagtaaagaaat--tgaataatttcaactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
upper sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 6
agcatattgagttttgcttcatttatgtggaatttgtatatataaggtcagggttacatattttatttt-gatgcaatgatggttgttacaaaattcacagGTGGTCACTTGGAGCTATTATGTACGAAATGCTGGTGGGATATCCTCCTTTTTATTCTGATGATCCAATGTTAACATGCAGGAAG
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agatccttggaactaaaacagagtgatttaaattattatggaaagtcagaacactccttaattttttccagaccaaattatgattcttttatt-tccacagGTGGTCACTTGGTGCTATCATGTATGAAATGCTTGTGGGGTATCCACCTTTTTATTCTGATGATCCCATGTCAACATGTAGGAAG
upper sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 6
agcatattgagttttgcttcatttatgtggaatttgtatatataaggtcagggttacatattttattttgatgcaatgatggttgttacaaaattc----acagGTGGTCACTTGGAGCTATTATGTACGAAATGCTGGTGGGATATCCTCCTTTTTATTCTGATGATCCAATGTTAACATGCAGGAAG
| | ||| | ||| || | | ||| ||| | | | | |||| || || | | | | ||| |||||||||||| ||||| || |||||||| |||||||| || || || ||||| || |||||||| || ||| ||| || | |||
aattactcgaga--tactttatactcgactaggttgggagg--aagccccgcatgttaggtttttgttcagcccagaacagttcaacatatgattttcctgcagGTGGTCACTAGGAGCAATCATGTACGAGATGCTGGTTGGTTACCCCCCTTTCTACTCTGATGAACCCATGACAACTTGTCGCAAG
upper sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------agcatattgagttttgcttcatttatgtggaatttgt-atatataaggtcagggttacatattttattttg-atgcaatgatggttgttacaaaattc---acagGTGGTCACTTGGAGCTATTATGTACGAAATGCTGGTGGGATATCCTCCTTTTTATTCTGATGATCCAATGTTAACATGCAGGAAG
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gtatgtgacaagtcgttctcctgaatctttctctttttatccttggctcatgatgtacttgcttagcttgataaagttcttgttgtgttcaaaaaggttgaacgtaagttttcctacagGTGGTCACTTGGAGCAATCATGTACGAGATGCTAGTTGGCTACCCTCCATTTTACTCTGACGAACCTATGACAACTTGTCGCAAGMapped 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|9986562|gb|BE660670.1|BE660670EST: ATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG GTGGTCACTTGGAGCTATTATGTACGAAATGCTGGTGGGATATCCTNCTTT
genomic: ATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTGgtgagtttta ... aaattcacagGTGGTCACTTGGAGCTATTATGTACGAAATGCTGGTGGGATATCCTCCTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtcagggttacatattttattttgatgcaatgatggttgttacaaaattcacagGTGGTCACTTGGAGCTATTATGTACGAAATGCTGGTGGGATATCCTCCTTTTTATTCTGATGATCCAATGTTAACATGCAGGAAG
ttttgat putative branch site (score: 4)
ttacatattttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcatattgagttttgcttcatttatgtggaatttgtatatataaggtcagggttacatattttattttgatgcaatgatggttgttacaaaattcacagGTGGTCACTTGGAGCTATTATGTACGAAATGCTGGTGGGATATCCTCCTTTTTATTCTGATGATCCAATGTTAACATGCAGGAAG
- - - - - - - tgcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatggtt