Sequence
atgc intronic sequence ATGC exonic sequence...atggaaagaaagacatagacttgttagccttgaaggttataatacttcttgagttttttgtagcatgaactagttaacatatgttgatgcttcttttcagATAAGTGTAGGATTGGATCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC
Basic information
species | Glycine max |
transcript | GLYMA15G42050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G42050.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g33940.1 (Oryza sativa), 3'ss of exon 2
------------------atggaaagaaagacatagacttgttagcc--ttgaaggttataatacttct----tgagtttt--ttgtagcatgaac----tagttaacatatgttgatgcttcttttcagATAAGTGTAGGATTGGATCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC
| || | | | || | ||||| | || | || | | |||| ||| || || | ||| | |||| || | || | | | | ||||| ||| ||||| || | ||||||||||| |||||||| ||||||||||| ||||||||||| ||||| || || || || || || || || || ||
gtaaaattgaaattgagcaatcaatcagtcagctcatctagctagccggccggagctagcaagcatgcaacagtgagatttagctgaagtttaaacatggtgattaatatttcatgtggtatatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACCGGGCGACGAC
upper sequence: GLYMA15G42050.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------------atggaaagaaagacatagacttg----ttagccttg-----aaggtta--taatacttcttgagttttttgta-gcatgaactagttaacatatgt--tgatgcttcttttcagATAAGTGTAGGATTGGATCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC
| ||| | | | | ||| ||| || || | | ||| || | | || | || | || | | ||||||||| | | ||| | | ||||| || |||||||| | ||| | ||| | |||||||| ||||||||||| ||||||||||| ||||| || || || || || || || || ||
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatattgattaacatatatatggttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
upper sequence: GLYMA15G42050.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G104074_T01 (Zea mays), 3'ss of exon 2
atggaaagaaagacatagacttgttagccttgaaggttataata-cttcttgagttttttgtag-catgaactagttaa--catatgttgatgcttcttttcagATAAGTGTAGGATTGGATCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC
| ||| | || | | |||| | | | ||| || || | | ||| | ||| | |||| || || | |||| | || | || || | |||||||| || |||||||| ||||||||||| ||||||||||| |||||||| ||||| ||||| || || || || ||
---tttaaaaatatatgaatctaa-agccaaaatatctcttataatttgaaaagaagtatataggtaactcataggaaggttatatatttgtggacaatggcagAAAGATGCAAAATAGGCACTGGGCCTCAAAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACGGGAACGAGAACGAACCGTGCCACGAC
upper sequence: GLYMA15G42050.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------------------atggaaagaaagacatagacttgttagccttgaaggttataatacttctt------------gagttttttgtagcatgaactagttaacatatgttga---tgctt-cttttcagATAAGTGTAGGATTGGATCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC
| || ||| | ||| |||| || | || || || ||| | | || | | || | |||||| || ||| | | | |||| | ||| ||||| || | |||| |||||| |||||||| ||||||||||| ||||||||||| ||||| || ||||| || || || || || || ||
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
upper sequence: GLYMA15G42050.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G155816_T01 (Zea mays), 3'ss of exon 2
atggaaagaaagacatagacttgttagccttgaaggttataatacttcttgagttttttgtagcatgaactagttaacatatgttgatgct---tcttttcagATAAGTGTAGGATTGGATC---AGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC
| || | ||| ||||| || || | | || | | ||| | | | | | | || || |||| ||| | | ||||| ||| |||||||| | | ||||||| | |||||||||||||||||||| ||||||| ||| ||||| || || || |||| || || || ||
---gtaactgactaata-acttgaatgcggtgtac-tagtagaaatctaagagctaataatgtctagtgtttcacaatatgtgttcatggtggacgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCAGCCACAAGGACAGGAAGTACCCTACGGGGACGCGAACCAACCGGGCGAC---
upper sequence: GLYMA15G42050.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G79580.1 (Arabidopsis thaliana), 3'ss of exon 2
atggaaagaaagacatagacttgttagccttgaaggttataat-acttcttgagttttttgtagcatgaactagttaacatatgttgatgcttcttttcagATAAGTGTAGGATTGGATCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC
|| | | ||| | | | | ||| |||||| | ||| |||||| | || || | ||||| || | | | ||| || || || || || || || ||||| || |||||||||||||| ||||| |||||||||||||| || || || ||| |||| || || || || |
-tgtgtgtttaaatatatatatatatatacttaagactataattaacaattgtattttttcaattatatttataacaaattttgttgttgtgtgtatgtagAGAAATGCAGAATCGGGTCGGGTCCTCAAAACGAGTGGTATTTCTTTAGCCACAAGGACAAGAAATATCCGACTGGGACCCGAACGAACCGGGCGACAGC
upper sequence: GLYMA15G42050.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0085g01210.t01 (Vitis vinifera), 3'ss of exon 1
-----atggaaagaaagacatagacttgttagccttgaaggttataatacttcttgagttttttgtagcatgaactagttaacatatgttgat---gcttcttttcagATAAGTGTAGGATTGGATCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC
| | || || | | | || ||| | ||| || | | ||| ||| ||| | || | | | | ||| | | | ||||||| || | ||||||||||| ||||||| |||||||||||||||||||| ||||| |||||||||||||| ||||| ||||||| |||||||| |
actaatcagtccgcaatacccaaa---agcaagattaaagttgatattattgc---agtacg--gtattgggaaatttttcatgtttttggatttggttggcatgcagATAAATGCCGAATTGGATCAGGCTCTCAGAACGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATACCCAACTGGAACTCGAACAAACCGAGCAACCAT
upper sequence: GLYMA15G42050.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
atggaaagaaagacat-----agacttgttagccttgaaggttataatacttctt--gagttttttgtagcatgaa----------ctagttaacatatgttgatgcttcttttcagATA------AGTGTAGGATTGGATCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC
| |||| | ||| | ||| | | ||| | || ||||| || | |||| | || || | ||| | || || || | | ||| | ||||| || | | ||| | |||||||| ||||||||||| || |||||||||||||| || || || || || || |||| ||
---gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: GLYMA15G42050.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
-------------------------atggaaagaaagacatagacttgttagccttgaaggttataatacttcttgagttttttgtagcatgaactagttaacatatgttgatgcttcttttcagATAAGTGTAGGATTGGATCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC
| | | | | | ||| | ||| | || | | || | || | || | | | || | | |||| ||| | ||||| || | | ||| | |||||||| ||||||||||| || |||||||||||||| || || || || || || |||| ||
gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaaccgtt--ctttggaagtctttgcgttctaaatgtctcttctctcactgcc--atcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttgagttttttgtagcatgaactagttaacatatgttgatgcttcttttcagATAAGTGTAGGATTGGATCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC
tgcttcttttc CT-rich tract
ttttttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atggaaagaaagacatagacttgttagccttgaaggttataatacttcttgagttttttgtagcatgaactagttaacatatgttgatgcttcttttcagATAAGTGTAGGATTGGATCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - aaagaaa
- - - - - - - - - - - - - -ccttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgatgc