Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgatgaaatcaattaactaaatttggctcttccctctttccccagagtaatgtcacctccaaattaaccttggtcttacacaatctttactaacttggataacaatcatcgacagGGTATCAAAGAAGGATGGTATGATGGAGGAAGCATTGCATTTGCTGTGATTCTTGTGATTGTTGTGACGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57110.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 6
gtttgtgatgaaat-caattaactaaatttggctcttccctctttccccagagtaatgtcacctccaaattaaccttggtcttacacaatctttactaacttggataacaatcatcgacagGGTATCAAAGAAGGATGGTATGATGGAGGAAGCATTGCATTTGCTGTGATTCTTGTGATTGTTGTGACGG
|| | | | | | ||| | | ||| || | ||| | | || | || ||| |||| ||| || | | | | |||| || |||||||| ||||||||||||| ||||||||| |||||||| | || || ||||||| || |
-----tggccatttgccacttactgtttatcgctgtttttttttttggtttgtagctataactttca--ttatttttggagttaattaactcctttt--------------ttgtgtgtagGGGATAAAAGAAGGCTGGTATGATGGAGCAAGCATTGCTTTTGCTGTTCTCCTAGTTGTTGTTGTTACAG
upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g08018.1 (Oryza sativa), 3'ss of exon 3
gtttgtgatgaaatcaattaacta-aatttggctcttccctctttcc-ccagagtaatgtcacctccaaattaaccttggtcttacacaatctttactaacttggataacaatcatcgacagGGTATCAAAGAAGGATGGTATGATGGAGGAAGCATTGCATTTGCTGTGATTCTTGTGATTGTTGTGACGG
|| | ||| | ||| | | | | || | |||| || | || || | || || || ||| | ||| || ||| || |||| ||||||||||||||||| || || | ||||||||||||||| || ||||||| || |||| || |
-----------tgtccacaaacgatggtttagttgagcaccctcactgccagcaaaacttttgatcagtgttttctttagttctaagt--tctgtcttaa-------aaaaat--tcattagGGCATCAAAGAAGGATGGTACGACGGTGCAAGCATTGCATTTGCGGTCTTTCTTGTCATACTTGTTACTG
upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 6
gtttgtgatgaaatcaattaactaaatttggctcttccctctttccccagagtaatgtcacctccaaattaaccttggtcttacacaatctttactaacttggataacaatcatcgacagGGTATCAAAGAAGGATGGTATGATGGAGGAAGCATTGCATTTGCTGTGATTCTTGTGATTGTTGTGACGG
| | || | | || |||| || | | | | | | || || | | | | || || | | ||| | ||||| | || || |||| || |||||||| ||||||||||||| |||||||| |||||||| |||| || | |||| || |
-------gcagatttcatcatattgccttatatctttcca-tgtgcttacattgattacattgc----tcatctgtgttcctttat----tttgca---ttggaatatgatgat-attagGGCATAAAAGAAGGCTGGTATGATGGAGCGAGCATTGCCTTTGCTGTTCTTCTAGTTGTATTTGTTACAG
upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G391042_T02 (Zea mays), 3'ss of exon 6
gtttgtgatgaaatcaattaactaaatttggctcttccctctttccccagagtaatgtcac--ctccaaattaaccttggtcttacacaatctttactaacttggataacaatcatcgacagGGTATCAAAGAAGGATGGTATGATGGAGGAAGCATTGCATTTGCTGTGATTCTTGTGATTGTTGTGACGG
| |||| | | ||| | | | | | || || | | | || | | | | || || ||||| | || | | |||| || |||||||| ||||||||||||| |||||||| |||||||| |||| || | |||| || |
---------------------gcagatttcatcatattcccttgcatctgtatgtgcttactgcttccattggtgctcatctgtgctcctttatttttacattggaatatgatga-cattagGGCATAAAAGAAGGCTGGTATGATGGAGCGAGCATTGCCTTTGCTGTTCTTCTAGTTGTATTTGTTACAG
upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 5
gtttgtgatgaaatcaattaactaaatttggctcttccctcttt--ccccagagtaatgtcacctccaaattaaccttggtcttacacaatctttactaacttggataacaatcat-cgacagGGTATCAAAGAAGGATGGTATGATGGAGGAAGCATTGCATTTGCTGTGATTCTTGTGATTGTTGTGACGG
|| ||||| ||| || | | || |||| | | | | ||| || || || | | | || || | ||| | ||||||||||| ||||||||||||||||| ||||||||||| ||||| || |||||||| |||||||| || |
---------------------ttatgtttggtcgttctcttgataatctaggattaatcgtatatttttgtgattgttgagattttt--attttcattcagtttgacgataattttgttgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATTCTTGTTATTGTTGTTACAG
upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 5
gtttgtgatgaaatcaattaactaaatttggctcttccctcttt--ccccagagtaatgtcacctccaaattaaccttggtcttacacaatctttactaacttggataacaatcat-cgacagGGTATCAAAGAAGGATGGTATGATGGAGGAAGCATTGCATTTGCTGTGATTCTTGTGATTGTTGTGACGG
| |||| ||| || | | || ||| | | | || ||| || || || | | || || || ||| | ||||||||||| ||||||||||||||||| ||||||||||| ||||| || |||||||| |||||||| || |
---------------------tgatgtttgatcgttctcttgataatctaggattaagagtatatttttgtgaatattgagattttt--attttcattctgtttgacaataattttgttgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATTCTTGTTATTGTTGTTACAG
upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 8
gtttgtgatgaaatcaattaactaaatttggctcttccctctttccccagagtaatgtcacctccaaattaaccttggtcttacacaatctttactaacttggataacaatcat-cgacagGGTATCAAAGAAGGATGGTATGATGGAGGAAGCATTGCATTTGCTGTGATTCTTGTGATTGTTGTGACGG
| ||| || | || | |||| | | || || || | |||| | | | | | |||| || || | ||| | |||||||| || |||||||||||||| || ||||||||||| ||||| || |||||||| ||| |||| || |
-------------tgtattt-ctcagttcatcccttcataatctg---ggattaggaacatgtttttgttaaacctag----gaattaggtttatcaagttcagaattaattctgtttcagGGTATTAAGGAAGGATGGTATGACGGGGGAAGCATTGCTTTTGCAGTTATTCTTGTTATTCTTGTTACAG
upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 5
gtttgtgatgaaatcaattaactaaatttggctcttccctctttccccagagtaatgtcacctccaaattaaccttggtcttacacaatctttactaacttggataacaatcat-cgacagGGTATCAAAGAAGGATGGTATGATGGAGGAAGCATTGCATTTGCTGTGATTCTTGTGATTGTTGTGACGG
||| | | | | | | | || || | | || | | | | | |||| || || ||| || |||||| | || ||||||||||||||||| ||||||||||| ||||| || |||||||| ||| |||| || |
---------------tgcatgctagac--agttttccttcataatctgggattaggaataagtttttgttgatgctag----gaattaggtttatcaagttcagacttaattatgtttcagGGTCTTAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATTCTTGTTATTCTTGTTACAG
upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 8
gtttgtgatgaaatcaattaactaaatttggctcttccctctttccccagagtaatgtcacctccaaattaaccttggtcttacacaatctttactaacttggataaca----atcatcgacagGGTATCAAAGAAGGATGGTATGATGGAGGAAGCATTGCATTTGCTGTGATTCTTGTGATTGTTGTGACGG
| ||| | | | | | | ||| || | || || || || | | | ||| | ||| || | || || ||||||| |||||||||||||||||||| || |||||||| ||||| || |||||||| || ||||| || |
--------------------atagaataatgatgcttctttataatccatgtgaaccatatatc----tttttattagtttcatttgagtttttatggcttccattttattttgtcttctttagGGTATTAAAGAAGGATGGTATGATGGGGGGAGCATTGCCTTTGCAGTTATTCTTGTTATAGTTGTTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaattaaccttggtcttacacaatctttactaacttggataacaatcatcgacagGGTATCAAAGAAGGATGGTATGATGGAGGAAGCATTGCATTTGCTGTGATTCTTGTGATTGTTGTGACGG
aatcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgatgaaatcaattaactaaatttggctcttccctctttccccagagtaatgtcacctccaaattaaccttggtcttacacaatctttactaacttggataacaatcatcgacagGGTATCAAAGAAGGATGGTATGATGGAGGAAGCATTGCATTTGCTGTGATTCTTGTGATTGTTGTGACGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA