Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtttcattgtaagagtatacgtatacacttctttttgatcattgtttgattcaatatctgttttttatattagGTTGCAAGTTTTGGTGCTTACCTCTTGAAGAGAGACATTATGGCTGTGTCTTTTGCTCCAAGAGACACTCATGAAGCTCAGGTACAGTTTGCTTTAGAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G10440.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G10440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G36550.1 (Glycine max), 3'ss of exon 1
--gtaagtgtttcattgtaagagtatacgt---------atacacttctttttgat--------cattgtttg-attcaatatctgttttttatatta-gGTTGCAAGTTTTGGTGCTTACCTCTTGAAGAGAGACATTATGGCTGTGTCTTTTGCTCCAAGAGACACTCATGAAGCTCAGGTACAGTTTGCTTTAGAAC
|| | || | | | | | | |||| ||| ||| |||| | ||| || | | ||| || || | | | ||||||||||| ||||||||||| ||||| |||||||| || ||| |||| ||||| |||||||| || |||||||| ||||| |||||||| || |||
tcgtgattgatcgaaaatcaaatcaaacgttaggactacatatgctttttttgtgtgtagggtgtgttgcttatacttaattccttcttgcactgtaaagGTTGCAAGTTGGGGTGCTTACCTTTTGAAAAGAGACATCATAGCTATGTCCTTTGCACCAAGAGATACACATGAAGCACAGGTCCAGTTTGCATTGGAAA
upper sequence: AT4G10440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G03000.1 (Glycine max), 3'ss of exon 1
gtaagtgtttcattgtaa---gagtatacgt-------atacacttctttttgat----------cattgtttg-attcaatatctgttttttatatta-gGTTGCAAGTTTTGGTGCTTACCTCTTGAAGAGAGACATTATGGCTGTGTCTTTTGCTCCAAGAGACACTCATGAAGCTCAGGTACAGTTTGCTTTAGAAC
|| ||| || || ||| | | |||| ||| | |||||| | ||| || | | ||| || || | | | |||||| |||| ||||||||||| |||| |||||||| | ||| |||||||||| |||||||| || |||||||| ||||| |||||||| || |||
-taggtgatttatcataatcaaatcaaacgttaggactatatatgcttttttggtgggaaggatgtgttgcttatacttaattccttcttgcactgtaaagGTTGCGAGTTGGGGTGCTTACCTTTTGAGAAGAGACATCCTAGCTATGTCTTTTGCACCAAGAGATACACATGAAGCACAGGTCCAGTTTGCGTTGGAAA
upper sequence: AT4G10440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0025g03200.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------gtaagtgtttcattgtaagagtatac----gtatacacttctttttgatcattgtttgattcaatatct--gttttttatatta-gGTTGCAAGTTTTGGTGCTTACCTCTTGAAGAGAGACATTATGGCTGTGTCTTTTGCTCCAAGAGACACTCATGAAGCTCAGGTACAGTTTGCTTTAGAAC
|| | || || || | | | || || | | | || | | | | ||| || | | ||| ||||||||| | ||||| ||| | || || || || ||| ||||| |||||||||| ||||||||||| |||||||| ||||| |||||||| |||| |
gtaagtaaaggcttcaactccttgtccatttaggccttctatattaccattgttttgtagtttattgcagtagctaacaggagtctcctactgtttcttgattgggtgtgttaagGTTGCAAGCTGGGGTGCCTACTTGTTAAAAAGGGATATTCTGGCTATGTCTTTTGCACCAAGAGACACACATGAAGCACAGGTCCAGTTTGCCCTAGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acgtatacacttctttttgatcattgtttgattcaatatctgttttttatattagGTTGCAAGTTTTGGTGCTTACCTCTTGAAGAGAGACATTATGGCTGTGTCTTTTGCTCCAAGAGACACTCATGAAGCTCAGGTACAGTTTGCTTTAGAAC
tctgtttttt CT-rich tract
tttgattcaatatctg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtttcattgtaagagtatacgtatacacttctttttgatcattgtttgattcaatatctgttttttatattagGTTGCAAGTTTTGGTGCTTACCTCTTGAAGAGAGACATTATGGCTGTGTCTTTTGCTCCAAGAGACACTCATGAAGCTCAGGTACAGTTTGCTTTAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA