Sequence
atgc intronic sequence ATGC exonic sequencegtcagaccctatttttcaaataacccaaatgccaaaatcttttttcttcttcttatacttcctctataaaagccttgaacttcacctatttttcatcttgtctcaataaaagaaagcaactttttgtttttgacattggggaatttggtgtgtagGTGTCGTGAGAAGCAGAGGAAGGAAGCTTCTCGGCTGCAGACAGTGAACAGAAAGCTGACTGCAATGAACAAGCTTTTAATGGAGGAAAATGACCGTTTG
Basic information
species | Glycine max |
transcript | GLYMA09G02750.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 1
gtcagaccctatttttcaaataacccaaatgccaaaatcttttttcttcttcttatacttcctctataaaagccttgaacttcacctatttttcatcttgtctcaataaaagaaagcaactttttgtttttgacattggggaatt----tggtgtgtagGTGTCGTGAGAAGCAGAGGAAGGAAGCTTCTCGGCTGCAGACAGTGAACAGAAAGCTGACTGCAATGAACAAGCTTTTAATGGAGGAAAATGACCGTTTG
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---------------------------------------------------------taacaagtattggaatcttgtgtattagaagacaccatcctttagatagtttattcatgta--cttttgccactgaaattgtgccttccttgtaattggcagATGCCGGGAGAAGCAGCGCAAGGAGGCCTCCCGGCTGCAAACTGTGAACCGGAAGCTGAATGCGATGAACAAGCTGTTGATGGAGGAAAATGACCGGCTG
upper sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 1
gtcagaccctatttttcaaataacccaaatgccaaaatcttttttcttcttcttatacttcctctataaaagccttgaacttcacctatttttcatcttgtctcaataaaagaaagcaactttttgtttttgacattggggaatttggtgtgtagGTGTCGTGAGAAGCAGAGGAAGGAAGCTTCTCGGCTGCAGACAGTGAACAGAAAGCTGACTGCAATGAACAAGCTTTTAATGGAGGAAAATGACCGTTTG
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---------------------------------aggatcgttgccacagttt-----cttcct-tgcaaatgatgt---ttttgtaactgtgtggtgtggtgtggccgacagttgatgatgtttttcctttg-------------tgatttgcagGTGCCGCGAGAAGCAGCGCAAGGAGGCATCTCGCCTGCAAACTGTGAACCGGAAGTTGACTGCGATGAACAAGCTGTTGATGGAGGAGAATGACAGGCTG
upper sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G023291_T01 (Zea mays), 3'ss of exon 1
gtcagaccctatttttcaaataacccaaatgccaaaatcttttttcttcttcttatacttcctc-tataaaagccttgaacttcacctatttttcatcttgtctcaataaaagaaagcaactttttgtttttgacattggggaatttggtgtgtagGTGTCGTGAGAAGCAGAGGAAGGAAGCTTCTCGGCTGCAGACAGTGAACAGAAAGCTGACTGCAATGAACAAGCTTTTAATGGAGGAAAATGACCGTTTG
|| | ||||| ||| || ||| ||| | || | || | | | | || ||| | | || | | | | ||| ||| | ||| | |||| || || ||||||||| ||||||| || || || |||||||| |||||| | ||||||||||| ||||||||||| || |||||||| |||||| | ||
--------------------------------------------tcgttgtcttagttttcttcatatgtaagtcagcaagtg-acatctgtaac-tcctgtgcgattt---gactgtgattctgatgtttc----ttgtga---ttgattggtagATGCCGCGAGAAGCAGCGGAAGGAGGCCTCGCGCCTGCAGACTGTGAACCGGAAGCTGACTGCGATGAACAAGCTGTTGATGGAGGAGAATGACAGGCTG
upper sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 1
gtcagaccctatttttcaaataacccaaatgccaaaatcttttttcttcttcttatacttcctctataaaagccttgaacttcacctatttttcatcttgtctcaataaaagaaagcaactttttgtttttgacattggggaatttggtgtgtagGTGTCGTGAGAAGCAGAGGAAGGAAGCTTCTCGGCTGCAGACAGTGAACAGAAAGCTGACTGCAATGAACAAGCTTTTAATGGAGGAAAATGACCGTTTG
|| | ||| | || | | | | ||| | | ||| | | | || ||| | | || ||| | | || |||| || || ||||||||| | ||||| | ||||| || || || |||||| | ||||||| ||| ||||||||||| || |||||||| |||||||| ||
----------------------------------------------aactacaagggaatcccgtgtattggaatccactgtttgctagctgtttgcttttttaggcgt--gcctgccactaaatcgtgtttccatcg-------tcgttggtagATGCCGGGAGAAGCAGCGCAAGGAGTCCTCTCGTCTACAAACCGTGAACCGGAAGCTGAGTGCGATGAACAAGCTGTTGATGGAGGAGAATGACCGGCTG
upper sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcagaccctatttttcaaataacccaaatgccaaaatcttttttcttcttcttatacttcctctataaaagccttgaacttcacctatttttcatcttgtctcaataaaagaaagcaactttttgtttttgacattggggaatttggtgtgtagGTGTCGTGAGAAGCAGAGGAAGGAAGCTTCTCGGCTGCAGACAGTGAACAGAAAGCTGACTGCAATGAACAAGCTTTTAATGGAGGAAAATGACCGTTTG
|| | | || || || | || | | | | ||| | ||| | | | | | ||||| ||| || ||| || ||| ||| ||||| |||||||||||||| || | |||| || |||||||||||||| ||||||| ||| |||||||||||||| ||||| || ||||| ||||||
---------------------------------------cttctgttcatttttctattatttcaacacatttatcatactgctataggtttgtctttaacttttctg-------gtttcttttggttgtt----ttgttgacttt-----ttagATGTCGAGAGAAGCAGAGGAAAGAGTCAGCTCGTCTTCAGACAGTGAACAGGAAGCTGAGTGCTATGAACAAGCTTTTGATGGAAGAGAATGATCGTTTG
upper sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcagaccctatttttcaaataacccaaatgccaaaatcttttttcttcttcttatacttcctctataaaagccttgaacttcacctatttttcatcttgtctcaataaaagaaagcaactttttgtttttgacattggggaatttggtgtgtagGTGTCGTGAGAAGCAGAGGAAGGAAGCTTCTCGGCTGCAGACAGTGAACAGAAAGCTGACTGCAATGAACAAGCTTTTAATGGAGGAAAATGACCGTTTG
||| | ||| || || | | ||| || | | || || || | | ||| || ||| || | | || || || |||||| || ||| |||||||||||||||||||| |||||| |||| || || |||||||||||||| || | ||| |||||||| || || ||||| || ||||| ||||||
----------------------------------ctgtctctgttcatccactaacatttcttcc-catcatccatgcac---atttggcttttatgttggcttagttggtctaacgaagcttcc--ttttgatttt---------------tagATGTCGTGAGAAGCAGAGGAAAGAAGCTGCTCGTCTTCAAACAGTGAACAGAAAACTCAATGCCATGAACAAACTCTTGATGGAAGAGAATGATCGTTTG
upper sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 1
gtcagaccctatttttcaaataacccaaatgccaaaatcttttttcttcttcttatacttcctctataaaagccttgaacttcacctatttttcatcttgtctcaataaaagaaagcaactttttgtttttgacattggggaatttggtgtgtagGTGTCGTGAGAAGCAGAGGAAGGAAGCTTCTCGGCTGCAGACAGTGAACAGAAAGCTGACTGCAATGAACAAGCTTTTAATGGAGGAAAATGACCGTTTG
|| | | | ||| || | || | ||| || | | || | | |||||| | | | |||| | || || | || | |||||| ||||| ||||| ||||||||||||||||| || ||||| ||||| | ||| ||||||||||||||||||| || ||||| || |||||||| ||
----------------------------------tgattatagcttctattcc-attcagtcttgaggaaaaatttagtgatggctgatgagcta--ctatctcaacccatg--------tgtttgctctt----tt------tctgtttaatagGTGCCGTGAAAAGCAAAGGAAGGAAGCTTCTCGTCTCCAGACTGTGAATCGGAAGTTGACTGCAATGAACAAGCTGTTGATGGAAGAGAATGACCGGTTA
upper sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S55_99V6.1 (Physcomitrella patens), 3'ss of exon 2
gtcagaccctatttttcaaataacccaaatgccaaaatcttttttcttcttcttatacttcctctataaaagccttgaacttcacctatt------tttcatcttgtctcaataaaagaaagcaactttttgtttttgacattggggaatttggtgtgtagGTGTCGTGAGAAGCAGAGGAAGGAAGCTTCTCGGCTGCAGACAGTGAACAGAAAGCTGACTGCAATGAACAAGCTTTTAATGGAGGAAAATGACCGTTTG
|||| || | |||| | | ||| || | || | || | | ||| | || | ||| | || || || |||||||| | |||||||| || || || | || || || || ||||| ||||||||||||||||||||||||| || || |
-------------------------------------------------------------aaaaggaaaaagactgcagttcatcagtgctcgggttttattctatcgctggttttagtagatattccttgaatgcgaacgaagttgctttaaatttcagATGCCGGGAGAAGCAACGCAAGGAAGCATCAAGGTTGGTTAGCGTCAATGCGAAACTTACTGCCCTGAACAAGCTTTTAATGGAGGAAAACGAGCGCCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcaataaaagaaagcaactttttgtttttgacattggggaatttggtgtgtagGTGTCGTGAGAAGCAGAGGAAGGAAGCTTCTCGGCTGCAGACAGTGAACAGAAAGCTGACTGCAATGAACAAGCTTTTAATGGAGGAAAATGACCGTTTG
ttttgac putative branch site (score: 3)
aactttttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagaccctatttttcaaataacccaaatgccaaaatcttttttcttcttcttatacttcctctataaaagccttgaacttcacctatttttcatcttgtctcaataaaagaaagcaactttttgtttttgacattggggaatttggtgtgtagGTGTCGTGAGAAGCAGAGGAAGGAAGCTTCTCGGCTGCAGACAGTGAACAGAAAGCTGACTGCAATGAACAAGCTTTTAATGGAGGAAAATGACCGTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA