Sequence
atgc intronic sequence ATGC exonic sequencegtaagtggaccaaatatgttttctttccactacgtattggttcttgcatgttggttggaagtaaaaccgttttgttttaaccgtttcacagGTGGTCAATCCATTTACCAAATATGCTTTGACCATATCTCCAGTAGCAATGAGTCTTGAGGAGTTGATACCATCAAGGCATATCAGGTCACATTGGTACG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39130.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39130.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G32260.1 (Glycine max), 3'ss of exon 9
gtaagtggaccaaatatgttttctttccactacgtattggttcttgcatgttggttggaagtaaaaccgttttgttttaaccgtttcacagGTGGTCAATCCATTTA---CCAAATATGCTTTGACCATATCTCCAGTAGCAATGAGTCTTGAGGAGTTGATACCATCAAGGCATATCAGGTCACATTGGTACG--------------------
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------tctttgaacaggttttttat--gtcatgtcatttctcttgcatttcta----aagtactcttacactgtg--agcaaagaaagatgttttttacttaattagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACCATCAAACCATGCCAAGTCTTATCTATATTCCATCTTCATCAGAACAGGG
upper sequence: AT2G39130.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G35280.2 (Glycine max), 3'ss of exon 8
gtaagtggaccaaatatgttttctttccactacgtattggttcttgcatgttggttggaagtaaaaccgttttgttttaaccgtttcacagGTGGTCAATCCATT--TACCAAATATGCTTTGACCATATCTCCAGTAGCAATGAGTCTTGAGGAGTTGATACCATCAAGGCATATCAGGTCACATTGGTACG--------------------
| || |||| | |||| | || | |||||||| | ||||| ||| | | | | || | | | | | || ||||| ||||| ||||||||||| ||||||||||| |||||||||||||| |||| ||| || ||| || ||
-------tgttatatcaattttagtcccac-atgtcatttctcttgcatttcta----aagtacttttacactgtgagcaaagaaagatgttttgt-acttaactagcatcacGTATGCATTGACTATATCTCCAGTGGCAATGAGTCTGGAGGAGTTGATACCGTCAAACCATGCCAAGTCTTATCTATATTCCATCTTCATCAGAACAGGG
upper sequence: AT2G39130.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G19430.1 (Glycine max), 3'ss of exon 7
gtaagtggaccaaatatgttttctttccactacgtattggttcttgcatgttggttggaagtaaaaccgttttgttt---taaccgtttcacagGTGGTCAATCCATTTACCA----AATATGCTTTGACCATATCTCCAGTAGCAATGAGTCTTGAGGAGTTGATACCATCAAGGCATATCAGGTCA-CATTGGTACG----
|| || || || || | | |||| || | | || || || | ||||| || | | || | | | | || || | | ||| || | || | | | | ||| |||| | || ||| || | || ||||| || | | |||
--aaatgagtcatgataattaatttatttcaatctatttgtacctacactgtgaaaataaagatcgatgtttttcttaattggcacccacatatgcattgagTCTATCTCCAGTAGCAATGTGTCTAGAGGA-GTTGATACCAACAAACAGTCCCAACTTTTTCATATATTCCAAGCTCATCAGAACAGCTCTAGTAGTTTCT
upper sequence: AT2G39130.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G15130.1 (Glycine max), 3'ss of exon 6
-gtaagtggaccaaatatgttttctttccactacgtattggttcttgcatgttggttggaagtaaaaccgttttgttttaaccgtttcacagGTGGTCAATCCATTTACCAAATATGCTTTGACCATATCTCCAGTAGCAATGAGTCTTGAGGAGTTGATACCATCAAGGCATATCAGGTCACATTGGTACG-------------
| | | |||| ||| | || | | || | | || || ||| | || || | | | | | | | | ||| |||||| |||| ||||||||||||||||| |||| ||||||||||||||| | | | || | ||
ttttaattttgaaaatgagttaagacagaattaaat-----tatttccgtttttattttttgtacctacattgtgaagataaagatagatgtttttcttaactagCACCCACATATGCATTGAGTCTATCTCCAGTAGCAATGTGTCTAGAGGAGTTGATACCAGCCAACAGTCCCAACTTTTTCATATATTCCAAGCTCATCAG
upper sequence: AT2G39130.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv13s0019g04660.t01 (Vitis vinifera), 3'ss of exon 10
----------gtaagtggaccaaatatgttttctttccactacgtattggttcttgcatgttggttggaagtaaaaccgttttgttttaaccgtttcacagGTGGTCAATCCATTTACCAAATATGCTTTGACCATATCTCCAGTAGCAATGAGTCTTGAGGAGTTGATACCATCAAGGCATATCAGGTCACATTGGTACG----------------
|||| | || ||| || | | || || | | || |||| | ||| | || || | | | | ||| |||||| || ||||| |||||||||||||||||||| || |||||||| || |||| || || || || ||| |
cagatgaagagtaaagcatttgagctctttcatttttttctttttttctttttttactttttttaaagaagaagaacagaa-------aatttttccttaattaga----------gCCACATATGCATTAACCATGTCTCCAGTAGCAATGAGTCTGGAAGAGTTGATCCCTTCAAACCAATCCAAATCTCACATGTATGCAATCCTCATTAGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggttcttgcatgttggttggaagtaaaaccgttttgttttaaccgtttcacagGTGGTCAATCCATTTACCAAATATGCTTTGACCATATCTCCAGTAGCAATGAGTCTTGAGGAGTTGATACCATCAAGGCATATCAGGTCACATTGGTACG
ttttaac putative branch site (score: 2)
ccgtttc CT-rich tract
ttttgttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtggaccaaatatgttttctttccactacgtattggttcttgcatgttggttggaagtaaaaccgttttgttttaaccgtttcacagGTGGTCAATCCATTTACCAAATATGCTTTGACCATATCTCCAGTAGCAATGAGTCTTGAGGAGTTGATACCATCAAGGCATATCAGGTCACATTGGTACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG