Sequence
atgc intronic sequence ATGC exonic sequencegtaaccctaagaatggcccttgacagctttgattttagtaacacgttgctcaatgatggtttatgtgtatctatttgtttcagAGATAGTAAACTGACAAGGTTGCTGAGGGATTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCTACAATATCACCTTCAGTATATTGTTTGGAAGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g02670.2 (Oryza sativa), 3'ss of exon 7
gtaaccctaagaatggc-ccttgacagctttgattttagtaacacgttg------ctcaatgatggtttatgtgt------atctatttgtttcagAGATAGTAAACTGACAAGGTTGCTGAGGGATTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCTACAATATCACCTTCAGTATATTGTTTGGAAGAG
|||| ||||| | | | || ||| ||||||| ||| |||| ||| | | | |||||| ||| || || ||||| ||||||||| ||||||||||| ||||| || || ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
gtaattctaaggacagtgtcctggcagatttgattctagaaacattttggcattttgccaagggtgtttatatgttgctccatttaattgttccagAGATAGCAAACTGACAAGATTGCTAAGAGACTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCCACAATATCACCTTCAGTATATTGTTTGGAAGAG
upper sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G40580.1 (Glycine max), 3'ss of exon 6
------gtaaccctaagaat----ggcccttgacagctttgattttagtaacacgttgctcaa------tgatggtttatgtgtatctatttgtt---tcagAGATAGTAAACTGACAAGGTTGCTGAGGGATTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCTACAATATCACCTTCAGTATATTGTTTGGAAGAG
||||| || | | | || || || |||| ||| || || | | || || | | ||||| || || |||| ||||| ||| | || || ||| |||||||||| ||||| || ||||| || || ||||||||||| |||||||| ||||| | | ||| |||||||
gtaagagtaactgcaacttttctagtcaattctcaatttcatttttcttaattatttcctggagtgattttattattaagatatatcttattattatatcagGGATAGCAAATTAACCAGATTGTTGAGGGATTCTTTGGGTGGTAAAACCAAAACGTGCATTATTGCCACAATATCCCCTTCCATTCACTGTCTGGAAGAA
upper sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G15520.2 (Glycine max), 3'ss of exon 5
---------gtaaccctaagaatggcccttgacagctttgattttagtaacacgttgctcaatgatggtttatgtgt---------atctatttgtttcagAGATAGTAAACTGACAAGGTTGCTGAGGGATTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCTACAATATCACCTTCAGTATATTGTTTGGAAGAG
| ||| | ||| | | | ||||||| || | || | | | || ||| | || || | |||| ||||| ||| | ||||| || |||||||||| ||||| || ||||| ||||| ||||| ||||||| ||||||||||| | | ||| |||||||
gtatgaatggctaccgttcttctggttatggtaacttttgattctattttcaaacctagagaaaaatgcttttgtattattaagatgtcccattatatcagGGATAGCAAATTAACAAGACTGTTGAGGGATTCCTTGGGCGGTAAAACCAAGACATGCATAGTTGCTACGATATCACCTTCTATTCACTGTCTGGAAGAA
upper sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G04830.1 (Glycine max), 3'ss of exon 5
------------gtaaccctaagaat-ggcccttgacagc-tttgattttagtaacacgttgctcaatg--atggtttatgtgtatctatttgtt---tcagAGATAGTAAACTGACAAGGTTGCTGAGGGATTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCTACAATATCACCTTCAGTATATTGTTTGGAAGAG
| ||| | | || | | ||| |||| | | || || || || | | ||||| || || |||||||||| ||| | || || ||| |||||||||| ||||| || ||||| || || ||||||||||| |||||||| ||||| | | ||| |||||||
gtatgagtaactgcaacttttcttgtcaattctcaatttcattttttttttattattttctgagtgattttattattaagatatatcttattattatatcagAGATAGCAAATTAACCAGATTGTTGAGGGATTCTTTGGGTGGTAAAACCAAAACGTGCATTATTGCCACAATATCCCCTTCCATTCACTGTCTGGAAGAA
upper sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0004g03810.t01 (Vitis vinifera), 3'ss of exon 6
---------------gtaaccctaagaatggcccttgaca-----gctttgattttag--taacacgttgctcaatgatggtttatgtgtatctatttgtt-tcagAGATAGTAAACTGACAAGGTTGCTGAGGGATTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCTACAATATCACCTTCAGTATATTGTTTGGAAGAG
|| | ||| ||| || | ||||||||| | | | ||| | | || | | | | | |||| ||||| ||| | |||||||| |||||||||| ||||||||||||||||| || ||||| ||||| |||||||| || || | | || |||||||||
gtatgaactgcataattagttcagtaaattattattggcatatgaggtttgattttgaacttagaaattgaggtgaggtaattaaaaagattgcctgaaatatcagGGATAGCAAATTAACAAGGTTATTGAGGGATTCCTTGGGAGGGAAAACAAAAACATGCATAATTGCCACAATATCGCCCTCCATTCACTGCTTGGAAGAG
upper sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S13_177V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------------gtaaccctaagaatggcccttgacagctttgattttagtaacacgttgctcaatgatggtttatgtgtatctatttgttt-cagAGATAGTAAACTGACAAGGTTGCTGAGGGATTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCTACAATATCACCTTCAGTATATTGTTTGGAAGAG
| | || | | | || || | || | | | ||| || || | | || | ||||||||| || |||||||| ||| | |||||||| |||||||| || |||||||| ||||||||||| || | || || || || |||| | |||||
gtaatttgtcctctgttgtgactatttgctggagtgacaaattccttcccagttttgtgttgattataattgtttctatttctattttcaactgtatgcctaatgtttctcttgacttcgtatggatacagAGATAGCAAGCTGACAAGATTGTTAAGGGATTCTTTGGGAGGAAAGACAAAGACCTGCATTATTGCCACCGTTTCGCCCTCCGTTCATTGCCTTGAAGAA
upper sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S6_143V6.1 (Physcomitrella patens), 3'ss of exon 6
-----gtaaccctaa---gaatggcccttgacagctttgattttagtaacacg-ttgctcaatgatggtttatgtgtatctatt---------tgtttcagAGATAGTAAACTGACAAGGTTGCTGAGGGATTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCTACAATATCACCTTCAGTATATTGTTTGGAAGAG
| | | ||| | | | || | || | | | | | || | ||| ||| | || | | ||| |||||||||||| |||||||| ||| | |||||||| |||||||| || ||||| || || || ||||| || | || || ||||| |||| | ||||||
gtagagcattcttaattgggaaaaacatttatgcctctagaatgaaggatgagctttcgtgatggctgttcctcacaattcactcttctttaatgtcacagAGATAGTAAGCTGACAAGATTGTTAAGGGATTCCTTGGGAGGAAAGACAAAAACGTGTATAATTGCCACCGTCTCGCCCTCAGTTCCTTGTCTCGAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattttagtaacacgttgctcaatgatggtttatgtgtatctatttgtttcagAGATAGTAAACTGACAAGGTTGCTGAGGGATTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCTACAATATCACCTTCAGTATATTGTTTGGAAGAG
tagtaac putative branch site (score: 1)
tttgtttc putative PPT
tatctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaccctaagaatggcccttgacagctttgattttagtaacacgttgctcaatgatggtttatgtgtatctatttgtttcagAGATAGTAAACTGACAAGGTTGCTGAGGGATTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCTACAATATCACCTTCAGTATATTGTTTGGAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA