Sequence
atgc intronic sequence ATGC exonic sequence...ttgaaaagtaaaccaattatcgttcctattggaagaatagttggttttccatgtaatattttagtaataaccaaatccttctcttttgcatgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTGTACACAGAAGAAAGCTGCATTGCCCGGGAAG
Basic information
species | Glycine max |
transcript | GLYMA06G13200.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G13200.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g15580.1 (Oryza sativa), 3'ss of exon 5
-----ttgaaaagtaaaccaattatcgttcctattggaagaatagttggttttccatgtaatattttagtaa--taaccaaatccttctcttttgcatgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTGTACACAGAAGAAAGCTGCATTGCCCGGGAAG
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ggtcattgatggcttaat--acaaagattcctagttagctgataatta-----ccggctatccctttagttaattaatcccttcattctttttctcaccatttgcagGTTCCAATGTTTGAAAACATGGATGAGAAGCTCTTGGATGCCATGTGTGATCGTCTAAAGCCCATGCTGTACACAGAAGGCAGCTGCATCATTCGCGAAG
upper sequence: GLYMA06G13200.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G148118_T02 (Zea mays), 3'ss of exon 6
--ttgaaaagtaaaccaat----tatcgttcctattggaagaatagttggttttccatgtaatattttagtaataaccaaatccttctcttttgcatgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTGTACACAGAAGAAAGCTGCATTGCCCGGGAAG
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gattcaatattatatctttctcttaatgtcatgttttaatgaacagttgccgtagcttactatgttattagcatggttaa-ccttttgctgctgtttgca-----gGTTCCAATGTTTGAAAACATGGATGAACAGCTGTTGGATGCCATGTGTGATCGTCTAAAGCCTATGCTGTACACAGAAGGAAGCTGCATCATTCGCGAAG
upper sequence: GLYMA06G13200.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G129375_T01 (Zea mays), 3'ss of exon 1
-------------------ttgaaaagtaaaccaattatcgttcctattggaagaatagttggttttccatgta---at--attttagtaataaccaaatccttctcttttgcatgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTGTACACAGAAGAAAGCTGCATTGCCCGGGAAG
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gcatgttctcatctcccccttttatagtaccttgagt-tcagcctagcagaaactttttttttattttgatgtatgtattgatcttcctaattttttttaccttgctgtgttcatcgtttccagGTTCCACTGTTTGAAAATATGGACGAACAGCTTTTGGATGCCATGTGTGACTGCCTAAAGCCCATTCTGTACACAGAAGGTAGCTGCGTTATTCGCGAAG
upper sequence: GLYMA06G13200.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv16s0050g02560.t01 (Vitis vinifera), 3'ss of exon 7
ttgaaaagtaaaccaattatcgttcctattggaagaatagttggttttccatgtaatatt--ttagtaataaccaaatccttctcttttgcatgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTGTACACAGAAGAAAGCTGCATTGCCCGGGAAG
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ttggtt--ttcagcattgtgtgttgtcttcaagttgattggtaatgcaccattaattattactaaaccatggatttacatctttttcttaaacattgttaagGTGCCAATGTTCGAAAAGATGGATGAGCAACTGATGGATGCAATGTGTGACCGTCTCAAGCCAGCACTGTACACAGAAGATAGCTACATCGTCCGGGAGGMapped 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|254345633|gb|GR855969.1|GR855969EST: ATTTAAGAAGGGATATTAAGCGGCATCTTTGCTTGGCTTTGCTGATGAGG GTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGAC
genomic: ATTTAAGAAGGGATATTAAGCGGCATCTTTGCTTGGCTTTGCTGATGAGGgtatgcttct ... tgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttccatgtaatattttagtaataaccaaatccttctcttttgcatgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTGTACACAGAAGAAAGCTGCATTGCCCGGGAAG
taataac putative branch site (score: 1)
tccttctcttttgcat putative PPT
taatattttagtaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgaaaagtaaaccaattatcgttcctattggaagaatagttggttttccatgtaatattttagtaataaccaaatccttctcttttgcatgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTGTACACAGAAGAAAGCTGCATTGCCCGGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- -aaaagtaa
- - - - - - - - - - - - cctattg
- - - - - - - - - - - - - - - - - - - -gttggtt
- - - - - - - - - - - - - - - - - - - - - - - - ccatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccaaa