Sequence
atgc intronic sequence ATGC exonic sequencegtatcacatgttccaccatagtgcccctattgatgtgtcttgtttcaatattggagcatttcataatttaatgaatgcaatctgttttggcttgtttgtgtcatgtggggacaaccagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGTGCATGTTTGGTTTCGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os12g02970.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g02970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G044004_T03 (Zea mays), 3'ss of exon 2
------------------------gtatcacatgttccaccatagtgcccctattgatgtgtcttgtttcaatattggagcatttcataat---------ttaatgaatgcaatctgttttggcttgtttgtgtcatgtggggacaac-----cagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGTGCATGTTTGGTTTCGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT
| | | | | | | | |||| | | | || || | || | || | || ||||| || | | | | | | | || | | ||||||||| ||| |||||| || ||||| ||||| |||||| ||||| ||||||| || ||||||||||||| |||| |||| |||||| | || ||
gtaccgggcacgccgccattattggggtttctcctctctctctctctctcctagtagcccagcccagtccagtaaacgggcgagcgaaaaaagaaaccgactgattgatgca-tcgatcgcgacgcgcacgcgccccgtctgtctctctttggcagCATGTACGGGCCGGTGCAGGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCGTCTACGCCGAGACGGTGAAGATCATCCTC
upper sequence: LOC_Os12g02970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G531064_T01 (Zea mays), 3'ss of exon 3
gtatcacatgttccaccatagtgcccctattgatgtgtcttgtttcaatattggagcatttcataatttaatgaatgcaatctgttttggcttgtttgtgtcatgtggggacaaccagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGTGCATGTTTGGTTTCGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT-------------------
| | | | | | | | | |||| | || | | || ||| | | ||| | | | | |||||| | ||| |||||| || ||||| ||||| |||||| ||||| ||||||| || |||||||||||| || |||| |||||| || ||
------------------------------aaacccgcccttctccgc--tcgttccgtttcgt--ttccacta--gccatccaataatg-ttgccccaccatcgatgtaccgagcagcatattcgggccggtgcagGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCATGTATGTCGAGACGGTGAAGGCCATCCTGAGCAAGGCAACCCGCACTT
upper sequence: LOC_Os12g02970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G535911_T03 (Zea mays), 3'ss of exon 7
gtatcacatgttccaccatagtgcccctattgatgtgtcttgtttcaatattggagcatttcataatttaatgaatgcaatctgttttggcttgtttgtgtcatgtggggacaaccagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGTGCATGTTTGGTTTCGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT-------------------
| |||| | | || ||||| | | || ||| | | ||| | | | | | || ||||| | ||| |||||| || ||||| ||||| |||||| ||||| ||||||| || |||||||||||| ||| |||| |||||| || ||
----------------aaacccgcccttctccgctcgttccgtttcgtttcca------ctagccatccaataa----------tgttgccccgccatcgatgtaccgaga-----agcatattcgggccggtgcagGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCATGTACGCCGAGACGGTGAAGGCCATCCTAAGCAAGGCAACCCGCACTT
upper sequence: LOC_Os12g02970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G346113_T01 (Zea mays), 3'ss of exon 2
gtatcacatgttccaccatagtgcccctattgatgtgtcttgtttcaatattggagcatttcataatttaatgaatgcaatctgttttggcttgtttgtgtcatgtggggac-aaccagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGTGCATGTTTGGTTTCGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT
|| ||| | ||| ||||| || || | | | |||| | || | | || || | | ||| || ||| |||| | |||||||| |||| |||||| |||||||| ||||| |||||| ||||| ||||||| || ||||||||||||| ||| |||| |||||| || ||
---gtacccagagcac-acgccgccattattggcccccctctgctccgc-tcgttccgtttcgt--ttccacta--gccgtccaataatg-ttgccc-tgccatcgatggaccgagcagCATGTTTGGGCCGGTGCAGGATGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACGCCGAGACGGTGAAGGCCATCCTG
upper sequence: LOC_Os12g02970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G166062_T01 (Zea mays), 3'ss of exon 7
gtatcacatgttccaccatagtgcccctattgatgtgtcttgtttcaatattggagcatttcataatttaatgaatgcaatctgttttggcttgtttgtgtcatgtggggacaaccagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGTGCATGTTTGGTTTCGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT
| | | |||| || ||| | | | || ||| | | | | | | || ||| | | ||| | | | | | |||||| | ||| |||||| || |||| |||||||||||| ||||| ||||||| || |||||||||||| || |||| |||||| || ||
-ttgccttttttccgccgccaaacccgcccttctccg-ctcgttccg-tttcgtttccactagccatccaataa----------tgttgccccaccatcgatgtaccgag-----cagCATATTCGGGCCGGTGCAGGACATGCGCATCCCATACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCATGTATGCCGAGACGGTGAAGGCCATCCTG
upper sequence: LOC_Os12g02970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G353762_T01 (Zea mays), 3'ss of exon 7
gtatcacatgttccaccatagtgcccctattgatgtgtcttgtttcaatattggagcatttcataatttaatgaatgcaatctgttttggcttgtttgtgtcatgtggggac-aaccagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGTGCATGTTTGGTTTCGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT
|| ||| | ||| ||||| || | ||| | |||| | || | | || || | | ||| | ||| |||| | |||||||| |||| |||||| || ||||| |||||||||||| ||||| ||||||| || |||| |||||||| || |||| |||||| || ||
---gtacccagagcac-acgccgccattattggcacccctgctccgctcattc---cgtttcgt--ttccacta--gccgtccaataatg-ttgccc-cgccatcgatggaccgagcagCATGTTTGGGCCGGTGCAGGACGTGCGCATCCCATACCAGCAGAAGCGCATGTTCGGCTTCGCCACCTTCGTGTATGCCGAGACGGTGAAGGCCATACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatttaatgaatgcaatctgttttggcttgtttgtgtcatgtggggacaaccagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGTGCATGTTTGGTTTCGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT
atttaat putative branch site (score: 4)
taatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcacatgttccaccatagtgcccctattgatgtgtcttgtttcaatattggagcatttcataatttaatgaatgcaatctgttttggcttgtttgtgtcatgtggggacaaccagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGTGCATGTTTGGTTTCGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC