Sequence
atgc intronic sequence ATGC exonic sequencegttacagagctaatacatgcatgatttgttgtacatggcgcttccaaaagctttccttcatactgattgctaccgcgctattttcctggtatgtagGGCCCTCGTGAGAAAGCTTTGGCATCATTTTCAGCTCTCTCAAGTGGTATTCTAGTTTGCACTGATGTTGCAGCAAGGGGTCTTGACATACCACATGTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g07080.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G303752_T03 (Zea mays), 3'ss of exon 5
---gttacagagctaatacatgcatgatttgttgtacatggcgcttccaaaagctttccttcatactgattgctaccgcgctatttt--cctggtatgtagGGCCCTCGTGAGAAAGCTTTGGCATCATTTTCAGCTCTCTCAAGTGGTATTCTAGTTTGCACTGATGTTGCAGCAAGGGGTCTTGACATACCACATGTTG
||| | | | | || | | | | ||||| | | ||| ||||||||||||| | | || |||| ||| |||| || ||| ||| ||||||||||||||||||||||| ||||| |||||||| ||||||| |||||||||||||||||||||||||||||||||||| |||||
tacattatttggatgtgatacaagtggtgttcta-atgacttccttcccagtggttttcttcatactgatttcatctatccttttttttcctaatatgcagAGCCTTCGAGAGAAAGCTTTGGCATCATTTTCTGCTCTTTCAAGTGGCGTTCTAGTCTGCACTGATGTTGCAGCAAGGGGTCTTGACATACCAAGTGTTG
upper sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G125947_T01 (Zea mays), 3'ss of exon 5
-gttacagagctaatacatgcatgatttgttgtac--atggcg--cttccaaaagctttccttcatactgattgctaccgcgctattttcctggtatgtagGGCCCTCGTGAGAAAGCTTTGGCATCATTTTCAGCTCTCTCAAGTGGTATTC--TAGTTTG-CACTGATGTTGCAGCAAGGGGTCTTGACATACCACATGTTG
|||||| | || | || ||| | ||| | ||||| | | ||| ||||||| ||||| | | | || ||||||| || | || ||| ||| ||||||||||||||||||||||| ||||| |||||| | || |||| ||| | | | || | || || |
cattacagtatctggatgtgatacaagtggtgttctaatgacttccttcccagtggttttcttcatattgatttc-atctatcttttttcctaatacgcagAGCCTTCGAGAGAAAGCTTTGGCATCATTTTCTGCTCTTTCAAGTTGCTTTTATTAGTCAATCACAGGGGCACCTTCATTGTATCAGTGAATTGGTTAAA---
upper sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G367714_T01 (Zea mays), 3'ss of exon 6
-------gttacagagctaatacatgcatgatttgttgt-acatggcgcttccaaaagctttccttcatactgattgctaccgcgctattttcctggtatgtagGGCCCTCGTGAGAAAGCTTTGGCATCA--TTTTCAGCTCTCTCAAGTGGTATTCTAGTTTGCACTGATGTTGCAGCAAGGGGTCTTGACATACCACATGTTG
|||||| | | | | |||| | | | ||| ||| | || | | | | | | | ||| | |||| || | | || | |||| | ||| || | | ||| || | | |||| | | || || | |||| ||| | ||
ttcctaatacgcagagccatcgagagaaagctttggcatcattttctgctctttcaagttgctttt---attagtcaatcacagggcaccttcattgtat-cagTGAATTGGTTA-AAAGTAGCGATTTCAGCTTCCCTGGTCTATCCATCTGGGTTCTCGAGGACTACGACTCAATAG-AGTGGGTTCTGAAGCATAGTCTGAGC
upper sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv13s0067g01900.t01 (Vitis vinifera), 3'ss of exon 5
-----gttacagagctaatacatgcatgatttgttgt--acatggcgcttcca-aaagctttccttcatactgattgctaccgcgctattttcctggtatgtagGGCCCTCGTGAGAAAGCTTTGGCATCATTTTCAGCTCTCTCAAGTGGTATTCTAGTTTGCACTGATGTTGCAGCAAGGGGTCTTGACATACCACATGTTG
|| ||| | || | ||||| ||| | | || | || | || || | | ||| || | | | || || | ||| | | |||||||| ||||| |||||| || |||| |||||||||||||| | || || ||||||||||| | || |||||||| || ||||
gtatatttgttgagacta-gcacacttgattagtttttaatattgaaattttatgaaactgatcattgcact--ttctggcttcttcactt--gtgttcaatagACTGCAAGGGAGAAAGCATTGGCTTCATTTACATCTCTTTCAAGTGGTATTCTTCTATGTACCGATGTTGCAGCTCGTGGACTTGACATTCCTGGCGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccaaaagctttccttcatactgattgctaccgcgctattttcctggtatgtagGGCCCTCGTGAGAAAGCTTTGGCATCATTTTCAGCTCTCTCAAGTGGTATTCTAGTTTGCACTGATGTTGCAGCAAGGGGTCTTGACATACCACATGTTG
tactgat putative branch site (score: 2)
ctattttcct putative PPT
tatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttacagagctaatacatgcatgatttgttgtacatggcgcttccaaaagctttccttcatactgattgctaccgcgctattttcctggtatgtagGGCCCTCGTGAGAAAGCTTTGGCATCATTTTCAGCTCTCTCAAGTGGTATTCTAGTTTGCACTGATGTTGCAGCAAGGGGTCTTGACATACCACATGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG