Sequence
atgc intronic sequence ATGC exonic sequencegttatctgtctttttgcatgtaacttattgttcaacttaattcgggtgccttcgtatgtttttattagcatatagtagtatttaccatttaataatttaaatatttgttgggccctgctagATCTTGAAGGAACTTCACAAATCTTGTCAAAAAGAAGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
Basic information
species | Glycine max |
transcript | GLYMA05G14170.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
gttatctgtctttttgcatgtaacttattgttcaacttaattcgggtgccttcgtatgtttttattagcatatagtagtatttaccatttaataatttaaatatttgttgggccctgctagATCTTGAAGGAACTTCACAAATCTTGTCAAAAAGAAGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
||| | || | || || | | |||| || | ||| || || | | ||| |||| | |||| |||| | | | |||| ||||| ||||||| || || ||||||||||||| ||||||||| | ||||| || || ||||| || ||||||||||| || |||||| | ||||| ||||
-------------gtgcttata-caagtttctctagtcaatt-ggttttctttacatattct------------gcagtcattac--tctaattattttgctcgtaacttcttcctg-tagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
upper sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 5
gttatctgtctttttgcatgtaacttattgttcaacttaattcgggtgccttcgtatgtttttattagcatatagtagtatttaccatttaataatttaaatatttgttgggccctgctagATCTTGAAGGAACTTCACAAATCTTGTCAAAAAGAAGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
||| || | | ||| || || ||| | ||| | | | | || ||| ||| || || || ||| |||| ||||||||||| || |||||||| |||| |||||||| | ||||| || || ||||| || ||||||||||| || |||||| | || || ||||
--------------------------------gtccttggatcattt-ctttcata-gtctttgatgcaataaatttgcttgtattattaaat----tacattcttactgg-------cagATATTGAAGGAACTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAAATACAAA
upper sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 5
gttatctgtctttttgcatgtaacttattgttcaacttaattcgggt--gccttcgtatgtttttattagcatatagtagtatttaccatttaataatttaaatatttgttgggccctgc-tagATCTTGAAGGAACTTCACAAATCTTGTCAAAAAGAAGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
| | ||||| | | | || | | | | | | || | || |||| || || | |||| | | |||| ||| |||| |||| | ||| |||| ||||| ||||||||||||||||||| || ||||||||| |||||||| || || |||||||| ||||||||||| |||||||| | ||||||||||
-----gtatttttttagccctgtttggtcagatgacgcattcctgctctgttctcatgtgcccttatatatatgtaaaacattttatta--tggtaatctaaggattt-ttggacactgaacagATTTTGAAAGAACTTCACAAATCTTGTCGAAGAGAAGATGGTACAGATGATCAAAAGAAAGGAACCCAACTTTTGGAAGTATATGCAATTGAGATTCAAA
upper sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 5
gttatctgtctttttgcatgtaacttattgttcaacttaattcgggtgccttcgtatgtttttattagcatatagtagtatttaccatttaataatttaaatatttgttgggccctgctagATCTTGAAGGAACTTCACAAATCTTGTCAAAAAGAAGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
|| ||| | || | | |||| | | | | ||| ||| || | | |||| |||| | ||| | | | | | | || | | | |||||||||||||| |||||||||||||||||||| |||||||||||||||||||| || || || || || || |||| || ||||| | || ||||| |
--------actccttg-gtatacatcagtgtt------atgtagaataacttt-tatagttgcact-gcat-cgtcagtagc-atcatatgtgatgctgaccaatggtcgtgtgtt--tagATCTTGAAGGAGCTTCACAAATCTTGTCAAAAGGAAGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGA
upper sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------gttatctgtcttttt---gcatgtaacttattgttcaactt--aattcgggtgccttcgtatgtttttattagcatatagtag--tatttaccatttaataattta-aatatttgttgg--gccctgc---tagATCTTGAAGGAACTTCACAAATCTTGTCAAAAAGAAGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
| | |||| | | || || || | ||| ||| | || | || | | || | ||||| | || | | || || ||| | | | | | | |||| |||||||| || || ||||||||||| || |||||||| ||||||||||| || || || || ||| | ||||||| ||||| |||||||||| |
gtaagtattctgcccgttgactcctcaactttattttcatatctttcaactttatctagtattgaatgatttcgtttactcggaataccagtacttttcaaaatgggatgtaatgtgtagtaaattccttgttctgagaaaacttgtgatactcacagcttgtcgtacgtgcagATTTTGAAGGAGCTCCATAAATCTTGTCAGAAGGAAGATGGTACAGATGACCAGAAGAAGGGCACACAATTGCTGGAGGTGTATGCGATAGAGATTCAGA
upper sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------gttatctgtctttttgcatgtaac---------ttattgttcaacttaattcgggtgccttcg---tatgtttttatt-agcatatagtagtatttaccatttaataatttaaatatttgttgggccctgctagATCTTGAAGGAACTTCACAAATCTTGTCAAAAAGAAGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
| || |||| | || || | | | | | | || ||| | | |||| ||| | || | |||| | | || | | || || || | | |||| |||| |||||||| || |||||||||||||| ||||||||||| |||||||| || || || || || ||| | | ||||| ||||| |||||||||| |
gtaagttcgctgccagttgatttctccacaatatcttcatatgtcctattttatctgataataaatgtcagtcgcttatctcaatgcttttcagttcgagatatatgttcgcagaatatattttttcgtacacaaatgtgagatgcttctaatttcttagaactgc-agATTTTGAAGGAGCTCCACAAATCTTGTCAGAAAGAAGATGGTACAGATGATCAGAAGAAGGGCACACAATTGCTCGAGGTTTATGCGATAGAGATTCAGAMapped 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|8283183|gb|BE020744.1|BE020744EST: AGCTTTGCAAGATATATTTTGATATTGGTGAATATGGGCGTATGAATAAG ATCTTGAAGGAACTTCACAAATCTTGTCAAAAAGAAGATGGCACAGATGAC
genomic: AGCTTTGCAAGATATATTTTGATATTGGTGAATATGGGCGTATGAATAAGgttatctgtc ... gccctgctagATCTTGAAGGAACTTCACAAATCTTGTCAAAAAGAAGATGGCACAGATGAC
EST:
gi|18690841|gb|BM519689.1|BM519689EST: AGCTTTGCAAGATATATTTTGATATTGGTGAATATGGGCGTATGAATAAG ATCTTGAAGGAACTTCACAAATCTTGTCAAAAAGAAGATGGCACAGATGAC
genomic: AGCTTTGCAAGATATATTTTGATATTGGTGAATATGGGCGTATGAATAAGgttatctgtc ... gccctgctagATCTTGAAGGAACTTCACAAATCTTGTCAAAAAGAAGATGGCACAGATGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcatatagtagtatttaccatttaataatttaaatatttgttgggccctgctagATCTTGAAGGAACTTCACAAATCTTGTCAAAAAGAAGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
atttaat putative branch site (score: 4)
ccctgct putative PPT
atagtagtatttacca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatctgtctttttgcatgtaacttattgttcaacttaattcgggtgccttcgtatgtttttattagcatatagtagtatttaccatttaataatttaaatatttgttgggccctgctagATCTTGAAGGAACTTCACAAATCTTGTCAAAAAGAAGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG