Sequence
atgc intronic sequence ATGC exonic sequence...ccatttgtgttgatattgtaaattgactaaattctattgacagaggttctgtttctgttttgcttattacaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCAGTGGAAGGACCAATCCCTCCATCAAAAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
Basic information
species | Glycine max |
transcript | GLYMA20G08360.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G08360.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g04020.1 (Oryza sativa), 3'ss of exon 6
ccatttgtgttgatattgtaaattgactaaattctattgacagaggttctgtttctgttttgcttattacaatctgt---ttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCAGTGGAAGGACCAATCCCTCCATCAAAAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
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--------gtaagtcacataagcttgatgatctatcgagcctgaaagttaaaatgaacagacagcaatctgatctgagaatttgcaaaatttgattgtcatagGTATGTTTCATGTGTGGTTGGTTGCCCTGTTGAAGGCACAATTCATCCATCAAAGGTAGCATATGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAG
upper sequence: GLYMA20G08360.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g04210.1 (Oryza sativa), 3'ss of exon 6
-ccatttgtgttgatattgtaaattgactaaattctattgacagaggttctgtttctgttttgcttattacaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCAGTGGAAGGACCAATCCCTCCATCAAAAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
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gtaagtcacataagcttgatgatctatcgagcctgaaagttaaaaagaacagacagcaatctgatc-tgagaatttgcata-----atttgatcgtcatagGTATGTTTCATGTGTGGTTGGTTGCCCTGTTGAAGGCACAATTCATCCATCAAAGGTAGCATACGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAG
upper sequence: GLYMA20G08360.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G175071_T01 (Zea mays), 3'ss of exon 5
--ccatttgtgttgatattgtaaattgactaaattctattgacagaggttctgtttctgttttgctta--ttacaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCAGTGGAAGGACCAATCCCTCCATCAAAAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
||| ||| ||||| || | | | || | | | | |||| || | | |||| | || | |||| ||||| ||| | |||||| || || || || |||||||||||||| || |||||| | || || ||||| || || |||||||| |||||||| ||||| ||||| |||| |||
taccacatgttttgatgtt-tgcacttacgtcactgaaatactttgggtt-tgctagatatgtgctgaagttgaataatgttgttctgtggcaaaaat--gtagGTACGTTTCTTGTGTGGTTGGATGCCCAGTAGATGGACCAGTGCCACCTTCAAACGTAGCTTATGTAGCGAAAGAACTTTATGACATGGGCTGCTATGAG
upper sequence: GLYMA20G08360.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 6
---------ccatttgtgttgatattgtaaattgactaaattctattgacagaggttctgtttctgttttgcttattacaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCAGTGGAAGGACCAATCCCTCCATCAAAAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
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atagaattaaccttttttccaatctccgaccctaacaaaacactaatagaagaaacagt-----tggtt--ctaataacagtctatgatt--atttcccaatattgaagGTATGTATCTTGCGTTGTGGGGTGTCCAGTAGAGGGACCTGTTCTACCCTCAAAAGTGGCTTATGTTGTGAAAGAACTCTATGACATGGGCTGCTTTGAG
upper sequence: GLYMA20G08360.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 5
---ccatttgtgttgatattgtaaattgactaaattctattgacagaggt--tctgtttctgttttgcttattacaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCAGTGGAAGGACCAATCCCTCCATCAAAAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
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ttactccatgtattaac-tcatgt-ttgaatgcttccaatgaaaagcaataatatgtttctgtttctgttactgaattgaagttg---gcattacattttgatagGTATGTGTCATGTGTCGTTGGGTGTCCGGTGGAAGGAGCTATTTCTCCCTCAAAAGTTGCATATGTGGCCAAAGAACTTTATGATATGGGTTGCTTTGAAMapped 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|23062483|gb|BU578511.1|BU578511EST: TATCGAGCTGTTACTCGGGCTGCTAAACAGCTCTCTATTCCTGTTCGAGG GTATGTATCATGCGTTGTTGGATGCCCAGTGGAAGGACCAATCCCTCCATC
genomic: TATCGAGCTGTTACTCGGGCTGCTAAACAGCTCTCTATTCCTGTTCGAGGgtatgccttt ... aatttcatagGTATGTATCATGCGTTGTTGGATGCCCAGTGGAAGGACCAATCCCTCCATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctgtttctgttttgcttattacaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCAGTGGAAGGACCAATCCCTCCATCAAAAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
tgtatttaaatttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccatttgtgttgatattgtaaattgactaaattctattgacagaggttctgtttctgttttgcttattacaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCAGTGGAAGGACCAATCCCTCCATCAAAAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
ccatttg
- - - -tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctgta