Sequence
atgc intronic sequence ATGC exonic sequence...atttcatttaatgcatttatatgtgtctatgctagctgagttttacttagaatcagaggggttatgtcaagtgttgagaatttttactagatgtgtgcagGCTGTTACTGTTCGTCCTTTATCTTCAGTAAGTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
Basic information
species | Glycine max |
transcript | GLYMA17G12950.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G12950.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------atttcatttaatgcatttatatgtgtctatgctagctgagttt-tacttagaatcagaggggt-tatgtcaagtgttgagaatttttactagatgtgtgcagGCTGTTACTGTTCGTCCTTTATCTTCAGTAAGTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
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gtaagtcttttgttgcaccctctacatggttgtctcctctggagtttcttt--tgcaagaccgcttctccttccttgctccctttatctttagcatgttagggttctaacttctttgctctgaatattttctt------ttcagGCTATCATTGTTCGACCTCTCTCAACAGTAAGTGCCCTTGTGCGATTTGCAGAAGAACCGCAGATGTTTGCATTCGAATTCAATGATGGTTGCCCGATTC
upper sequence: GLYMA17G12950.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G367023_T01 (Zea mays), 3'ss of exon 4
---att-tcatttaatgcatttatatgtgtctatgctagctgagttttacttagaatcagaggggttatgtcaagtgttgagaatttttactagatgtgt--gcagGCTGTTACTGTTCGTCCTTTATCTTCAGTAAGTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
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aagataatcagtccttagggtagaatatatataagaga-ctcagct--aatatgggccatatgggccttaacacttacttg---tttgcactgaatttctttccagGCTGCCATTGTACGACCACTCTCAGCAGTAAGTGCTTTTGTTCGATTTGCTGAAGAGCCACAGATGTTTGCATTTGAATTCAATGATGGCTGCCCAATTC
upper sequence: GLYMA17G12950.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G049288_T01 (Zea mays), 3'ss of exon 4
atttcatttaatgcatttatatgtgtctatgctagctgagttttacttagaatcagaggggttatgtcaagtgttgagaatttttactagatgtgtg--cagGCTGTTACTGTTCGTCCTTTATCTTCAGTAAGTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
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-----------------------------------------------------------------ataggttcttacttgtttgcactgaatttctttccagGCTGTCATAGTACGACCACTCTCAGCAGTAAGTGCTCTTGTTCGATTTGTAGAAGAACCACAGATATTTGCATTTGAATTCAATGATGGCTGCCCAATTC
upper sequence: GLYMA17G12950.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 4
-----atttcatttaatgcatttatatgtgtctatgctagctgagttttacttagaatcagaggggttatgtcaagtgttgagaatttttactagatgtgtgcagGCTGTTACTGTTCGTCCTTTATCTTCAGTAAGTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
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tttgagttgtgcttaa-aaagacat-tgtgcaaaggatagttatgttt---ctatatgtttgatggttatgtcaagtgttaagaatctcaattagatgtgtgcagGCTGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTC
upper sequence: GLYMA17G12950.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S60_221V6.1 (Physcomitrella patens), 3'ss of exon 4
atttcatttaatgcatttatatgtgtctatgctagctgagttttacttagaatcagaggggttatgtcaagtgtt------gagaatttttactagatgtgtg-cagGCTGTTACTGTTCGTCCTTTATCTTCAGTAAGTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
|| | | | | | || || | | || | | | || | || || | | | | | | ||| ||||| || | ||| || |||||||| | || || |||||||||||||||||| || ||||| |||||||| ||||| || | |||||| ||||| | |
-------ccaaagaaaaaagaaaaagaaaataaagaaaagacaaaatagaaagaaagaaaatcagctcctgcatttctctggaaactaacaaatggttctgtttcagGCGGTCATTGTCCGATCTTTATCTGCGGTGGCTGGTCTTGTTCGGTTTGCTGAGGAACCCCAAATGTTTGCGATTGACTTCAATGATGGTTGCCCTCTTC
upper sequence: GLYMA17G12950.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ35138 (Selaginella moellendorffii), 3'ss of exon 5
--atttcatttaa---tgcatttatatgtgtctatgctagctgagttttacttagaatcagaggggttatgt-caagtgttgagaattt-ttactagatgt--gtgcagGCTGTTACTGTTCGTCCTTTATCTTCAGTAAGTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
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gtatttctctacagtttgcattcaagcgtgattgtttt--tttagctttcttcaaaacttgcctgagtgcatgctggtgttaacaggtcattgatggttgatggaacagGCAGTGAGTGGTCGGCCTCTATCGTCAGCAGCAGCTCTCGTTCGATTTGCTGAGGAGCCCCAGATGTTTGCTATTGAGTTTGGTGATGGATGCCCAGTCC
upper sequence: GLYMA17G12950.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ24089 (Selaginella moellendorffii), 3'ss of exon 5
--atttcatttaa---tgcatttatatgtgtctatgctagctgagttttacttagaatcagaggggttatgt-caagtgttgagaattt-ttactagatgt--gtgcagGCTGTTACTGTTCGTCCTTTATCTTCAGTAAGTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
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gtatttctctacagtttgcattcaagcgtgattgtttt---ttagctttcttcaaagcttgcctgagtgcatgctgttgttaacaggtcattgatggttgatggaacagGCAGTGAGTGGTCGGCCTCTATCGTCAGTAGCAGCTCTCGTTCGATTTGCTGAGGAGCCCCAGATGTTTGCTATTGAGTTTGGTGATGGATGCCCAGTCCMapped 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|298191220|gb|HO038699.1|HO038699EST: TCATTCTTACAAAGGTTTCACTTGTGGAAAGGCGTCCTGAGAATTATGAA GCTGTTACTGTTCGTCCTTTATCTTCAGTAAGTGCCCTTGTTCGGTTTGCT
genomic: TCATTCTTACAAAGGTTTCACTTGTGGAAAGGCGTCCTGAGAATTATGAAgtaagtgacg ... atgtgtgcagGCTGTTACTGTTCGTCCTTTATCTTCAGTAAGTGCTCTTGTTCGGTTTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttagaatcagaggggttatgtcaagtgttgagaatttttactagatgtgtgcagGCTGTTACTGTTCGTCCTTTATCTTCAGTAAGTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
aatttttactagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttcatttaatgcatttatatgtgtctatgctagctgagttttacttagaatcagaggggttatgtcaagtgttgagaatttttactagatgtgtgcagGCTGTTACTGTTCGTCCTTTATCTTCAGTAAGTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - -tgcattt
- - - - - - - - - -tatgtgt
- - - - - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - agagggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgag