Sequence
atgc intronic sequence ATGC exonic sequencegtaagcatctacaaaatatataaaaactgtaaaagcataacaatatattatctctaatgttatcttcctttgtaaagACCATCCATGGATCAAGGAGGATGGAGAGGCACCAGATGTTCCTCTTGATAATGCGGTGATGTCCAGGCTCAAACAATTCAAAGCAATGAACAATTTCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G12180.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G12180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G04010.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------gtaagcatctacaaaatatataaaaactgtaaaagcataacaatatattatctctaatgttatcttcctttgtaaagACCATCCATGGATCAAGGAGGATGGAGAGGCACCAGATGTTCCTCTTGATAATGCGGTGATGTCCAGGCTCAAACAATTCAAAGCAATGAACAATTTCAA
| | | | | | | || | | || ||| || | || | | | | |||| || | ||| |||||||||||||||||||||||||| ||||||||| |||||||| ||||| || || ||||||||||| |||| |||||||||| | |||||
gtgcgtataatattgacttcctttctatgaacatcttgaattcaactaggaattcttgatttgcaaattaattttactttagcccagacaaattggttcaatgcaattctaataaagtcttttttatttttttattttgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAATGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACCAATTCAA
upper sequence: AT5G12180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G44720.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------gtaagcatctacaaaatatataaaaactgtaaaagcataa--caatatattatctctaatgt-tatcttcctttgt-------aaagACCATCCATGGATCAAGGAGGATGGAGAGGCACCAGATGTTCCTCTTGATAATGCGGTGATGTCCAGGCTCAAACAATTCAAAGCAATGAACAATTTCAA
| | || || | || | | | || | |||| | | ||| | || || |||| | | ||| |||||||||||||||||||||||||| ||||||||| |||||||| || || || || ||||||||||| |||| |||||||||| | |||||
gtacgtataatattgacttcctttctatgaattcgactacatgttcttgatttacatattaattttactatagcccgggcagattggttcaatgcaattctaataaagcacattttactttatgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAACGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACGAATTCAA
upper sequence: AT5G12180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------------gtaagcatctacaaaatatataaaaactgtaaaagcataacaatatattatctctaatgttatcttcctttgtaaagACCATCCATGGATCAAGGAGGATGGAGAGGCACCAGATGTTCCTCTTGATAATGCGGTGATGTCCAGGCTCAAACAATTCAAAGCAATGAACAATTTCAA
| | || ||||| | | ||| || | | ||| || ||| | | | | | | ||| ||||||||||||||||||||||| || ||||||||| || ||||| ||||| || || ||||| |||||||||| |||||||||| | |||||
gtaagcatatatcctccactgtttttgtttcaccttcaatcaattattttttttacaaaccgcttgaattcacttacaatttcatgatttactaacgaaat-tgattata-ataatcggcgaacgtgttatgttaaaaacagATCATCCATGGATCAAGGAGGATGGCGAAGCACCAGATAAACCACTTGACAATGCTGTACTGAATAGGCTGAAACAATTCAGAGCAATGAACCAATTCAA
upper sequence: AT5G12180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G08140.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------gtaagcatctacaaaatatataaaa-actgtaaaagcataacaatat--attatctctaatgttatcttcctttgtaaagACCATCCATGGATCAAGGAGGATGGAGAGGCACCAGATGTTCCTCTTGATAATGCGGTGATGTCCAGGCTCAAACAATTCAAAGCAATGAACAATTTCAA
|| | ||| || | || | |||| || | ||| || ||| | | || | | | | ||| ||||| |||||||||||||| || || ||||||||| |||||||| ||||| || || |||||||||||||| | |||||||||| | |||||
gtaagcactcattattcttcgctgtttttgtttcaccttcaattctttgtcttactagtcgcttgaatcctcttataatttcatgatttactggggaaattaatcaactctaataatcaatgaacttgttatgttaaaaacagATCATCCTTGGATCAAGGAGGACGGCGAAGCACCAGATAAGCCTCTTGACAATGCTGTACTGAATAGGCTCAAACAATTTAGAGCAATGAACCAATTCAA
upper sequence: AT5G12180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0009g03150.t01 (Vitis vinifera), 3'ss of exon 3
---------gtaagcatctacaaaa----tatataaaaac-tgtaaaagcataacaata--tatta------tctctaatgttatcttcctttgtaa-agACCATCCATGGATCAAGGAGGATGGAGAGGCACCAGATGTTCCTCTTGATAATGCGGTGATGTCCAGGCTCAAACAATTCAAAGCAATGAACAATTTCAA
| | || || ||| | | | || | | || || | || ||| | ||| || || ||| | ||| ||||||||||| |||||||||||||| ||||| ||| ||||||||| ||||| || | ||| ||||||| || | |||||||||||| |||||
actgagtttggagatatttaggaaaactttgtttgaagtcatacttaattatgatgttagccattgcacatttttctgataaaattcaattttttcttagATCATCCATGGATTAAGGAGGATGGAGAAGCACCTGATACTCCTCTTGACAATGCAGTTTTTGAAAGGTTCAAACAGTTTAGAGCAATGAACAAGTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaactgtaaaagcataacaatatattatctctaatgttatcttcctttgtaaagACCATCCATGGATCAAGGAGGATGGAGAGGCACCAGATGTTCCTCTTGATAATGCGGTGATGTCCAGGCTCAAACAATTCAAAGCAATGAACAATTTCAA
ctctaat putative branch site (score: 3)
tgttatcttccttt CT-rich tract
ataacaatatattatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcatctacaaaatatataaaaactgtaaaagcataacaatatattatctctaatgttatcttcctttgtaaagACCATCCATGGATCAAGGAGGATGGAGAGGCACCAGATGTTCCTCTTGATAATGCGGTGATGTCCAGGCTCAAACAATTCAAAGCAATGAACAATTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA