Sequence
atgc intronic sequence ATGC exonic sequence...attgctataaattgttggcatgcttttgctgtaatttttctccatttccataactgttctcttttcatttttctcattttgttaatggtgcatggtacagACCGTTGTTTTCTGTCTAGTGGATATTTATATCATGCTTGGGAAAGCATTTTTGCCATATTTGGAAGGGCTTAACAGCACACAGTTGAAGTTGGTCACCA
Basic information
species | Glycine max |
transcript | GLYMA10G04850.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 20
-attgctataaattgttggcatgcttttgctgtaatttttctccatttccataactgttctcttttcatttttctcattttgttaatggtgcatggtacagACCGTTGTTTTCTGTCTAGTGGATATTTATATCATGCTTGGGAAAGCATTTTTGCCATATTTGGAAGGGCTTAACAGCACACAGTTGAAGTTGGTCACCA
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aaatgtctcaacctgctatagttcttgcattttcaccatgaatcaattcgtgatgcatcatcccggttcatatctgatagtattgttttcatatttt-tagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA
upper sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os02g40430.1 (Oryza sativa), 3'ss of exon 21
--attgctataaattgttg-gcatgcttttgctgtaatttttctccatttccataactgttctcttttcatttttctcattttgttaatggtgcatggtacagACCGTTGTTTTCTGTCTAGTGGATATTTATATCATGCTTGGGAAAGCATTTTTGCCATATTTGGAAGGGCTTAACAGCACACAGTTGAAGTTGGTCACCA
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gtgtaataatatatgactatgtgcacgtttaatacatatcacctttaaaaaaatgaatgttttgtgtttggaat-ctgatatcgtattcactttct--tccagACTGTTGTATTCTGCTTGGTGGATATCTACATTATGCTTGGGAAAGCATTTGTACCATATCTAGAGGGGCTTAATAGCACGCAGCTGCGCCTAGTAACAA
upper sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 20
-------------------------attgctataaattgttggcatgcttttgctgtaatttttctccatttccataactgttctcttttcatttttctcattttgttaatggtgcatggtacagACCGTTGTTTTCTGTCTAGTGGATATTTATATCATGCTTGGGAAAGCATTTTTGCCATATTTGGAAGGGCTTAACAGCACACAGTTGAAGTTGGTCACCA
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gtcagtaccatcatattttccttgctttgcattattctgtaggtaccgaccttttcttatatcttgaaatttc-ataa-tacattgctctaatgacttatccttgtcaaattttttttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTTGCTCCATACTTGGAAGGGCTTAGCAGCACGCAGCTCCGCCTAGTAACCA
upper sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 20
lower sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 20
--------attgctataaattgttggcatgcttttgctgta--atttttctccatttccat--aactgttctcttttcatttttctcattttg------ttaatggtgcatggtacagACCGTTGTTTTCTGTCTAGTGGATATTTATATCATGCTTGGGAAAGCATTTTTGCCATATTTGGAAGGGCTTAACAGCACACAGTTGAAGTTGGTCACCA
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gtaaaggaattgaaaaaaaaaacttgacttttctactcataccagtaacttacgatttgatgaaattggacaagttataactaactctctatgagggggtctttgctgtttgttgcagACAGTGGTGTTCTGTCTAGTAGACATATATATAATGCTTGGGAAAGCATTTTTGCCGTATTTGGAAGGTCTAAACAGCACGCAGGTTCGTCTAGTGACCA
upper sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 17
attgctataaattgttggcatgcttttgctgtaatttttctccatttccata-actgttctcttttcatttttctcattttgttaatggtgcatggta-cagACCGTTGTTTTCTGTCTAGTGGATATTTATATCATGCTTGGGAAAGCATTTTTGCCATATTTGGAAGGGCTTAACAGCACACAGTTGAAGTTGGTCACCA
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--catcatatgacaaagttgtgcttaaatacatgatattctacctatgcatgcatttatattttattttgtatattgatttattttgagtctgtgttggcagACTGTTGTATTCTGTCTAGTGGACATCTATATCATGCTTGGGAAAGCTTTTTTGCCATACCTGGAGGGGCTTAACAGCACACAATTGCGGTTGGTGACGAMapped 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|7796593|gb|AW781990.1|AW781990EST: TGCCTGCTTTGTTTGAAGCTTTTGGAAACCAGAGTGCTGATGTTCGCAAG ACCGTTGTTTTCTGTCTAGTGGATATTTAT
genomic: TGCCTGCTTTGTTTGAAGCTTTTGGAAACCAGAGTGCTGATGTTCGCAAGgtacttaggc ... catggtacagACCGTTGTTTTCTGTCTAGTGGATATTTAT
EST:
gi|9899206|gb|BE608104.1|BE608104EST: TGCCTGCTTTGTTTGAAGCTTTTGGAAACCAGAGTGCTGATGTTCGCAAG ACCGTTGTTTTCTGTCTAGTGGATATTTATATCATGCTTGGGAAAGCATTT
genomic: TGCCTGCTTTGTTTGAAGCTTTTGGAAACCAGAGTGCTGATGTTCGCAAGgtacttaggc ... catggtacagACCGTTGTTTTCTGTCTAGTGGATATTTATATCATGCTTGGGAAAGCATTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccataactgttctcttttcatttttctcattttgttaatggtgcatggtacagACCGTTGTTTTCTGTCTAGTGGATATTTATATCATGCTTGGGAAAGCATTTTTGCCATATTTGGAAGGGCTTAACAGCACACAGTTGAAGTTGGTCACCA
tgttaat putative branch site (score: 3)
atttttctcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgctataaattgttggcatgcttttgctgtaatttttctccatttccataactgttctcttttcatttttctcattttgttaatggtgcatggtacagACCGTTGTTTTCTGTCTAGTGGATATTTATATCATGCTTGGGAAAGCATTTTTGCCATATTTGGAAGGGCTTAACAGCACACAGTTGAAGTTGGTCACCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- tgctata
- - - - - - - - -gcatgct
- - - - - - - - - - - - - tgctgta
- - - - - - - - - - - - - - - - - - - - -ccatttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatggtg