Sequence
atgc intronic sequence ATGC exonic sequencegtactcttcttctgtcatttgatttgaggtttattttggtttggttgctgagaatggtttgattaccttgtcagcgagattttatgtgatttagatttctctgccaccaagcatggcagagttttataactttctggctgctcgaactgattgttttcgtaatatttgaacagCGAAAGCTTGCCCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
Basic information
species | Glycine max |
transcript | GLYMA08G22140.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 2
gtactcttcttctgtcatttgatttgaggtttattttggtttggttgctgagaatggtttgattaccttgtcagcgagattttatgtgatttagatttctctgccaccaagcatggcagagttttataactttctggctgctcgaactgattgttttcgtaatatttgaa-cagCGAAAGCTTGCCCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
| ||| || || || || |||| || | | ||| | || || | | | | ||| | |||| | || ||| ||| | |||| ||| |||| | || ||||| || |||||||| || ||||||||||| ||||| |||||||||||
-------------------------------------------------------gtattgtttcgatttccatttagtttttttgagggatttctttttatgtcattc-----------gctctgtttttttttcgctgtgttgataatttctttgcgttgtttttggttcagAGAAAATTAGCGCAAAGGTCTGAGAGAGTTAAATCTGTGGATCTTCATCCTACAGAACCATG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 6
gtactcttcttctgtcatttgatttgaggtttattttggtttggttgctgagaatggtttgattaccttgtcagcgagattttatgtgatttagatttctctgccaccaagcatggcagagttttataactttctggctgctcgaactgattgttttcgtaatatttgaacagCGAAAGCTTGCCCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
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-------------------------------------------------------------------------------------gtaatgcagtctcctttgatgctcgatttcatccttaatcattcttattcgg--gactgtattgacacgcttctttgt-tttgatcagCGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 2
gtactcttcttctgtcatttgatttgaggtttattttggtttggttgctgagaatggtttgattaccttgtcagcgagattttatgtgatttagatttctctgccaccaagcatggcagagttttataactttctggctgctcgaactgattgttttcgtaatattt-gaacagCGAAAGCTTGCCCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
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------------------------------------------------------------------------------gtattgcttatctttcaactttctgcttc------tgtta---ttttatta--ttatagctgtggtcataatttgcttttgttatgttttgatcagAGAAAGTTTGCTCAACGATCAGAGAGAGTCAAATCTGTTGATCTGCATCCTACTGAACCATG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 2
gtactcttcttctgtcatttgatttgaggtttattttggtttggttgctgagaatggtttgattaccttgtcagcgagattttatgtgatttagatttctctgccaccaagcatggcagagttttataactttctggctgctcgaactgattgttttcgtaatatttgaacagCGAAAGCTTGCCCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
||||| ||| || | | | | ||| | | | ||| || ||| | | | | | | |||||| || || | || | | || | | | |||| ||| |||| ||||| |||||||| || |||||||| || ||||||||||||||||| ||||||||
------------------------------gtatttatgttcatccacttgaatttatcttgtta---ggctaataaatgtttccatgctttgtaatccagttatatc--------tttagttttcaaaagttgtagcgttt--agctaacaatg-----acctgttgatcagAGAAAACTTGCACAAAGATCTGAAAGAGTAAAATCAGTGGATCTACATCCAACTGAACCATG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 2
gtactcttcttctgtcatttgatttgaggtttattttggtttggttgctgagaatggtttgattaccttgtcagcgagattttatgtgatttagatttctctgccaccaagcatggcagagttttataactttctggctgctcgaactgattgttttcgtaatatttgaacagCGAAAGCTTGCCCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
|| | |||| | || ||| |||||| | ||| ||||| ||| | ||||| | | | | | ||| || | | ||| || | | ||| || || ||| | || || || |||||||||||||||||||| ||||||||||| |||||| | || |||||
------------------------------gtacgcttgtttattccctttgaa----ttgatttctatgta---cagatta-----gatctcgatttgtttaatgtttaata-gttgaagtattgatgtcattttgcttctggta--------------aattttggatcagAGGAAACTCGCGCAAAGATCAGAGAGAGTAAAATCTGTGGATCTGCATCCATCTGAGCCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagttttataactttctggctgctcgaactgattgttttcgtaatatttgaacagCGAAAGCTTGCCCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
ttttcgtaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactcttcttctgtcatttgatttgaggtttattttggtttggttgctgagaatggtttgattaccttgtcagcgagattttatgtgatttagatttctctgccaccaagcatggcagagttttataactttctggctgctcgaactgattgttttcgtaatatttgaacagCGAAAGCTTGCCCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA