Sequence
atgc intronic sequence ATGC exonic sequence...catgttttgcttacactaggctatgctactcttattcacatgagaactacgaatgctggaaaatggtctgtttctaattcatctttgcctcctggaacagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTTATCATGAAGACACTTAGAGAACGCGAAGAAACAGCAA
Basic information
species | Glycine max |
transcript | GLYMA02G17070.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G17070.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g22580.1 (Oryza sativa), 3'ss of exon 4
catgttttgcttacactaggctatgctactcttattcacatgagaactacgaatgctggaaaatggtctgtttctaattcatctttgcctcctggaa-cagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTTATCATGAAGACACTTAGAGAACGCGAAGAAACAGCAA
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gtaatttttcttaccataag-------aatttt-tttacgtgatcaat-tgtatgctgatgcaag---tgcgctaagatgagatagttcacttgcattcagATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA
upper sequence: GLYMA02G17070.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G143253_T01 (Zea mays), 3'ss of exon 4
catgttttgcttacactaggctatgctactcttattcacatgagaactacgaatgctggaaaatggtctgtttctaattcatc----tttgcctcctggaacagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTTATCATGAAGACACTTAGAGAACGCGAAGA-AACAGCAA
| ||| | | | | |||| | || | || | ||||| | | | | | |||| ||| ||||| ||||||||| |||||||| || || ||||||||||| ||||||||||||||||| ||||| || | || | || |||||| | |||||||| || |
-gtatttccttcttgccaagtc------ctctaacacat-cgtcgaccttgtttgctgtgacacttgtgctaacaagaacatcgaaattttcctcc--atacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG-
upper sequence: GLYMA02G17070.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 3
catgttttgcttacactaggctatgctactcttattcacatgagaactacgaatgctggaaaatggtctgtttctaattcatctttgcctcctggaacagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTTATCATGAAGACACTTAGAGAACGCGAAGAAACAGCAA
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--------gtaaaaacaaagtta----acctttgttca---atgaataagaatcactgagtagttactaacatttgattcttgcat-tctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA
upper sequence: GLYMA02G17070.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
catgttttgcttacactaggctatgcta--ctcttattcacatgagaactacgaatgctggaaaatggtctgtttctaattcatctttgcctc-ctggaacagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTTATCATGAAGACACTTAGAGAACGCGAAGAAACAGCAA
| | | | || || | |||| || | || | |||| | | | | | | |||| | | | |||||||||||||| | || || ||||||||||| ||||||||||||||||| || ||||| || |||| || ||||| || ||||| ||||||| |
--------gttgatattaaatcttgaaaatttcttgttttagctaatgctttggtccatggatttcaataaataga-actccttttttgtttgatttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
upper sequence: GLYMA02G17070.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S107_15V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------------------------------------------catgttttgcttacactaggctatgcta------ctcttattcacatgagaactacgaatgctggaaaatggtctgtttctaattcatctttgcctcctgga--acagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTTATCATGAAGACACTTAGAGAACGCGAAGAAACAGCAA
|||| | | ||| || | || | || || | | | ||| | || | |||| | | | || | | || || |||||| |||||| ||||| || ||||||||||| ||||||||||||||||| | || || | || | ||| | | || || | | ||
gtatagagcacctcttcggtggtctctttcttttgaaactagtttagagctaaaactgtgtagcgtgttgtctcccgtgttttctcatgatctttgcacattatttcagcctcgaaggtcgtttgttgttagttggtgttcgatctgttgacgaaggtcatctctttgataatttgagtttcttgccctgcagATGGTTGATCCGCTAACGGCTCTGATGCATGCCGTTCAAGTGATGAACTTGTTGAAAACTTTGATTCTACGCACATTGAAGGACCGGAAGGCTACTTTGC
upper sequence: GLYMA02G17070.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S60_256V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------------------catgttttgcttac---actaggctatgctactcttattcacatgagaactacgaatgctggaaaatggtctgtttctaatt-catctttgcctcctggaacagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTTATCATGAAGACACTTAGAGAACGCGAAGAAACAGCAA
| |||| | | | | | | | | ||| | | | | || || | |||| | || | ||| | | | | |||||| ||||||| || || || ||||||||||| |||||||| |||||||| ||||| || || || | ||||| | || || | | ||
gtatagtgttgtttctacgcttttcacccagagaagctgatgaccattacaagatcagactcgtagagatttcactacagatgctgtcttcgacgtttcatgtgctgaatttgaacgtaggtattccgtgtttatg-gtgtttcaattgttgtagaatgtgtaacatttattgacattgcttcattatccttcagATGGCTGATCCACTGACAGCTCTGATGCATGCTGTTCAAGTCATGAACTTGCTCAAAACTCTGATTCTTCGCACACTGAAGGACCGAAAGGCCACTTTGCMapped 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|298194653|gb|HO043125.1|HO043125EST: AAATGAATGCAAGAAATATTGCAATGGTTTTTGCACCAAACATGACTCAG ATGCCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTA
genomic: AAATGAATGCAAGAAATATTGCAATGGTTTTTGCACCAAACATGACTCAGgtatcctcac ... cctggaacagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTA
EST:
gi|193445615|gb|FK411670.1|FK411670EST: AAATGAATGCAAGAAATATTGCAATGGTTTTTGCACCAAACATGACTCAG ATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAAC
genomic: AAATGAATGCAAGAAATATTGCAATGGTTTTTGCACCAAACATGACTCAGgtatcctcac ... cctggaacagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actacgaatgctggaaaatggtctgtttctaattcatctttgcctcctggaacagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTTATCATGAAGACACTTAGAGAACGCGAAGAAACAGCAA
ttctaat putative branch site (score: 2)
ttcatctttgcctcct CT-rich tract
tttctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catgttttgcttacactaggctatgctactcttattcacatgagaactacgaatgctggaaaatggtctgtttctaattcatctttgcctcctggaacagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTTATCATGAAGACACTTAGAGAACGCGAAGAAACAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
catgttt
- - - -tgcttac
- - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - - -acatgag
- - - - - - - - - - - - - - - - - - - - - - - - - gaatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttgcc