Sequence
atgc intronic sequence ATGC exonic sequencegtaagcagctcttatcttaaaagctcctatatatatttcattgaactcttcttgacatttttgttgttttaaagATCATCCATGGATCAAGGAGGATGGAGAAGCACCGGATGTTCCTCTTGACAATGCAGTGATGTCTAGGCTCAAGCAGTTCAAAGCAATGAACAACTTTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G19360.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G19360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G04010.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------gtaagcagctcttatctta--------aaa--gctcctatatatatttcattgaactcttcttgacatttttgttgttttaa----agATCATCCATGGATCAAGGAGGATGGAGAAGCACCGGATGTTCCTCTTGACAATGCAGTGATGTCTAGGCTCAAGCAGTTCAAAGCAATGAACAACTTTAA
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gtgcgtataatattgacttcctttctatgaacatcttgaattcaactaggaattcttgatttgcaaattaattttactttagcccagacaaattggttcaatgca-attctaataaagtcttttttatttttttattttgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAATGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACCAATTCAA
upper sequence: AT5G19360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G44720.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------gtaagcagctcttatcttaaaagctcc-tatatatatttcattgaactcttcttg---acatttttgttgttttaaa-----gATCATCCATGGATCAAGGAGGATGGAGAAGCACCGGATGTTCCTCTTGACAATGCAGTGATGTCTAGGCTCAAGCAGTTCAAAGCAATGAACAACTTTAA
|| | || | || | | | || || || || ||| | ||||||| || | | || ||||||||||||||||||||||||||||||||||| ||| ||||||||||| ||||| || ||||||||| ||||||| |||||||||| | || ||
gtacgtataatattgacttcctttctatgaattcgactacatgttcttgatttacatattaattttactatagcccgggcagattggttcaatgcaattctaataaagcacattttactttatgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAACGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACGAATTCAA
upper sequence: AT5G19360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------gtaagcagctcttat---cttaaaagctccta---tatatatttcattga--actcttcttgacatttttgttgttttaaa----gATCATCCATGGATCAAGGAGGATGGAGAAGCACCGGATGTTCCTCTTGACAATGCAGTGATGTCTAGGCTCAAGCAGTTCAAAGCAATGAACAACTTTAA
|| | ||| || |||| || || | || | ||||| | | | | | |||| | ||||| |||||||||||||||||||||||||| |||||||| ||| || ||||||||||| || || |||||| || || |||| |||||||||| | || ||
gtaagcatatatcctccactgtttttgtttcaccttcaatcaattattttttttacaaaccgcttgaattcacttacaatttcatgatttactaacgaaattgattataataatcggcgaacgtgttatgttaaaaacagATCATCCATGGATCAAGGAGGATGGCGAAGCACCAGATAAACCACTTGACAATGCTGTACTGAATAGGCTGAAACAATTCAGAGCAATGAACCAATTCAA
upper sequence: AT5G19360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G08140.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------gtaagcagctcttatcttaaaagctcctatatatatttcattgaactcttcttgacatt---tttgttgttttaaa----gATCATCCATGGATCAAGGAGGATGGAGAAGCACCGGATGTTCCTCTTGACAATGCAGTGATGTCTAGGCTCAAGCAGTTCAAAGCAATGAACAACTTTAA
| | | | | || | | | | || | ||| | | |||||| | || | ||||| | ||||| |||||||| |||||||||||||| || |||||||| ||| |||||||||||||| || || ||||||||| || || | |||||||||| | || ||
gtaagcactcattattcttcgctgtttttgtttcaccttcaattctttgtcttactagtcgcttgaatcctcttataatttcatgatttactggggaaatt--aatcaactctaataatcaatgaacttgttatgttaaaaacagATCATCCTTGGATCAAGGAGGACGGCGAAGCACCAGATAAGCCTCTTGACAATGCTGTACTGAATAGGCTCAAACAATTTAGAGCAATGAACCAATTCAA
upper sequence: AT5G19360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0009g03150.t01 (Vitis vinifera), 3'ss of exon 3
-----------------gtaagcagctcttatcttaaaagctcctatat----atatt--tcattgaac-tcttcttgacat--ttttgttgttttaaagATCATCCATGGATCAAGGAGGATGGAGAAGCACCGGATGTTCCTCTTGACAATGCAGTGATGTCTAGGCTCAAGCAGTTCAAAGCAATGAACAACTTTAA
|| | | || | | || | || || || || ||||| || | || ||| | || || ||| ||||||||||||||| |||||||||||||||||||| ||| |||||||||||||||||| | ||| |||| ||||| | |||||||||||| || ||
actgagtttggagatatttaggaaaactttgtttgaagtcatacttaattatgatgttagccattgcacatttttctgataaaattcaattttttcttagATCATCCATGGATTAAGGAGGATGGAGAAGCACCTGATACTCCTCTTGACAATGCAGTTTTTGAAAGGTTCAAACAGTTTAGAGCAATGAACAAGTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagctcctatatatatttcattgaactcttcttgacatttttgttgttttaaagATCATCCATGGATCAAGGAGGATGGAGAAGCACCGGATGTTCCTCTTGACAATGCAGTGATGTCTAGGCTCAAGCAGTTCAAAGCAATGAACAACTTTAA
tcttgac putative branch site (score: 3)
tttttgtt CT-rich tract
tatatatatttcattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcagctcttatcttaaaagctcctatatatatttcattgaactcttcttgacatttttgttgttttaaagATCATCCATGGATCAAGGAGGATGGAGAAGCACCGGATGTTCCTCTTGACAATGCAGTGATGTCTAGGCTCAAGCAGTTCAAAGCAATGAACAACTTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA