Sequence
atgc intronic sequence ATGC exonic sequencegtaaagtttcatttttggttttgaagtaacctttttctaatcttttttctttgcctaattgcttggttttggtcttagATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G60690.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 4
----------------------gtaaagtttcatttttggttttgaagtaacctttttctaatcttttttctttgcctaattgcttggt-tttggtcttagATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG
| | || ||| ||| ||| | || | | | | | | | | ||| ||| | | | | || ||| | || ||||| ||||||||||| ||| |||||||||| || |||||||| || || ||| |||||||||| ||||||||||||||||||
gtaagtaaatagttctgagtgactcaggtagaattattg---ttggatggacttgctctttcgatatcatgctatcttaactgccttttatcttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 3
-----------------gtaaagtttcatttttggt---tttgaagtaacctttttctaat----------cttttttctttgc---ctaattgcttggttttggtcttagATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG
|| |||| |||||| || |||| | |||| | ||||||| ||| || || |||| ||| ||| | || |||| || |||||||| || |||||||||| |||||||||||||| ||||||||||||||||| | |||||||||||||||
gttagtgaaatttcctttgaatgttttggttttgggcaattggaagcggctgccctctagggattggtttgccattttcttgataaactagttatatgatttttgtcc-agACTCCTTACAATTGCGGAGGAGACCCTGACAGAGTTCCTCTCCAAGGCTACAGGGACTGCTGTTGATTGGGTGCCAATGCCTGGGATGAAG
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G469551_T02 (Zea mays), 3'ss of exon 4
----------------------------gtaaagtt---tcatttttg----gttttgaagtaacctttttctaatcttttttctttgcctaattgcttggttttggtcttagATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG
|| || | ||| || |||| | ||| | | | || | | | | || |||||| | || | || |||| ||||||||||| ||| |||||||||| || ||||||||||| |||||| |||||||||| ||||||||||||||||||
gtaagtaaactgtaaaccagagcttgctgtgaaactctctcacttcaatagtgtttaataagaacgtactgttgatacatgatactaaacc--ttttccacttttgggcc-agGCTCCTTGCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACAGGGACTGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 4
----------------------gtaaagtttcatttttggttttgaagtaacctttttctaatcttttttctttgcctaattgctt-ggttttggtcttagATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG
| || ||| ||| | || | |||| | || | | | | | || | || | ||| | || | || ||||||||||| || |||||||||| || |||||||| || || ||| |||||||||| ||||||||||||||||||
gtaagtgaatcattctggccatctggagaaggattcttgttgcgtaaccttgccatttcaagactatcctaatcataataccattccaattcttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G042250_T03 (Zea mays), 3'ss of exon 4
----------------------gtaaagtttcatttttggttttgaagtaacctttttctaatcttttttctttgcctaattgc---ttggttttggtcttagATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG
| || ||||||| | |||||||| | | | || | || | | | | | || | ||| | || | || || |||||||| || |||||||||| || |||||||| || || ||| |||||||||| ||||||||||||||||||
gtaagtgaatcgttctggccatctggagaaggatttttgttgc----gtaaccttgccattgagactgtcctaatcatagtgccatttcaaatcttgtttcagACTCCTTGCGATTGCGGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 3
gtaaagtttcatttttggttttgaagtaacctttttc-taatc--ttttttctttgcctaattgcttggttttggtctt---agATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG
|||| | | || | |||||| | | ||| | | |||| || | || | ||| || || | ||| | || ||||| |||||||| |||||| |||||||||| || |||||||||||||||||||| |||||||| ||||||||||||||||||
gtaattctgaacttcatgaagtgaagttgcttcttttgtggtgaagttttgctcaaattggtttttctgttgtgatccttgcagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
gtaaagtttcatttttggttttgaagtaacctttttc-taatc--ttttttctttgcctaattgcttggttttggtctt---agATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG
||||| | || | || ||| | | ||| | | |||| || | || | ||| | || | ||| | || ||||| |||||||| |||||| |||||||||| || |||||||||||||||||||| |||||||| ||||||||||||||||||
gtaaatctgagcttcatgaagtggagttgcttcttttgtggtgaagttttactcaaatttgtttttctgttgcgatccttgcagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0019g04320.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------gtaaagtttcatttttggttttga---agtaacctttttctaatcttttttctttgcctaattgcttggttttggtct-tagATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG
||| | | || ||||| | | | || | ||||| ||| | | | || | || || ||| || | |||||||| || |||||| | ||| |||||||| || ||||||| |||||||||||||||||||| ||||| ||||||||||||
gtaatgttaaccatcagcaatattgacctctgtagaactccacttttgatgtaggtttgctatcattttttcaattgcagctgctgatgcacttaatcctttatgttctacagGCTCCTCTCAATAGCTGAGGAGGCCATGGGGGAGTTCCTTTCAAAGGCTAAGGGAACTGCTGTTGATTGGGTCCAGATTCCTGGGATGAAG
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 3
------------gtaaagtttcatt-----tttggttttgaagtaacctttt--tctaatcttttttctttgcctaattgcttggttttggtcttagATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG
||| | ||| | ||| | | || | | || | | | || | | | ||| ||| | ||| | ||| | ||||| || |||||||||||||||||||||||||| || |||||||||||||||||||| |||||||| ||||||||||||||||||
gtaatgtctaatacaaatgtccatcagttctctggctatttctctacatgtggatccattgtaattcagtggtatgatttctttgcttt--ttgcagACTCCTCTCCATTGCAGAGGAGACTTTGGCAGAGTTCCTCTCAAAGGCTACAGGAACTGCTGTCGATTGGGTCCAGATGCCTGGGATGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtaacctttttctaatcttttttctttgcctaattgcttggttttggtcttagATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG
tttttctaatcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagtttcatttttggttttgaagtaacctttttctaatcttttttctttgcctaattgcttggttttggtcttagATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG