Sequence
atgc intronic sequence ATGC exonic sequence...attaggagtcttgagggtacccctaattatggtccccgacaagtttgagtacctatgtcatgattttatttgatgttgtgttgtggtaattcatctttagGGTTATGTTATGTACCTTGTCCGTGTGAGGCATGGTGGTAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G302876_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 2
attaggagtcttgagggtacccctaattatggtccccgacaagt-ttgagtacctatgtcatgattttatttgatgttgtgttgtggtaattcatctttagGGTTATGTTATGTACCTTGTCCGTGTGAGGCATGGTGGTAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC
| | | |||| | ||| || | | | || || | ||| || || | | | |||| || | || | |||||||||| | |||| |||||||||||||| |||||| ||||||||||| |||||||| |||||||||| ||||||||||||||||||||||||||||
gggtgctcccatttatttaccaatttatataatcacatttgaatattttgtcctgtaatcaaaatattgtgcttaactat-ttgtcgttacctttcctcagGGTTATGTGGTTTACCGTGTCCGTGTGAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTACGGCAAGCCCAAGCACCAGGGTATCACCC
upper sequence: GRMZM2G302876_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 2
-attaggagtcttgagggtacccctaatt-atggtccccgacaagtttgagtacctatgtcatgattttatttgatgttgtgttgtggtaattcatctttagGGTTATGTTATGTACCTTGTCCGTGTGAGGCATGGTGGTAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC
| | | | | || | || | | |||| | | || || || | | | || || | || |||| ||||| | |||| ||| || || |||| |||||| ||||||||||| |||||||| |||||||||||||||||||||||||||||||||| ||||
agccaaaatgtattcacatgctgctgtctgattcacttttgaatgttttggccctataatccaaatattgtgcataactattttttgac--cttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATTACCC
upper sequence: GRMZM2G302876_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv15s0021g02480.t01 (Vitis vinifera), 3'ss of exon 2
-attaggagtcttgagggt---acccctaattatggtccccgacaagtt--tgagtacctatgtcatgattttatttgatgttgtgttgtggtaattcatctttagGGTTATGTTATGTACCTTGTCCGTGTGAGGCATGGTGGTAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC
|| | | ||| ||| | | | || | | |||| ||| | | | ||||| || ||| | | ||| ||||||| |||||||| || | ||| ||||| || | ||||||| ||||||||||| | |||||| | ||||| ||||| ||||| | |||||||| ||||||
tgtttaaaattatgacaaactggcccattaatttgataagcatcaagacgatgattctttttactttgattata----atgccaaacactatt--ttctattttagGGGTATGTTATCTATCGTGTTCGTGTTAGACGTGGTGGTCGGAAGAGGCCTGTTCCCAAGGGCATTGTTTATGGAAAGCCTACAAACCAGGGTGTCACCC
upper sequence: GRMZM2G302876_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv00s0551g00020.t01 (Vitis vinifera), 3'ss of exon 2
---attaggagtcttgag--ggtacccctaattatggtccccgacaagtttgagtacctatgtcatgattttatttgatgttgtgttgtggtaattcatctttagGGTTATGTTATGTACCTTGTCCGTGTGAGGCATGGTGGTAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC
| | ||| || || | || || | || | ||| || || || || | ||| || | | | || |||||||||| || || | ||| ||||| || | ||||||| ||||||||||| |||||||| | ||||| ||||| ||||||| |||| ||| | ||||
tctaatcactctctcgatccagttctgctgcttgtaatct---ataagcctggaattggttgctat-atctacacaaatgacactctg-gatgtactgttttcagGGTTATGTGATTTATCGTGTTCGTGTTAGACGTGGTGGTCGGAAGAGGCCTGTGCCCAAGGGAATTGTTTATGGTAAGCCCACAAACCAAGGTGTTACCC
upper sequence: GRMZM2G302876_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S7_364V6.1 (Physcomitrella patens), 3'ss of exon 2
-----attaggagtcttgagggtacccctaattatggtccccgaca-agtttgagtacctatgtcatgatt-ttatttgatgttgtgttgtg-gtaattcatctttagGGTTATGTTATGTACCTTGTCCGTGTGAGGCATGGTGGTAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC
| | | | | | || | | || | | | || ||||| || | || ||| | | | | |||| || | ||||||| || |||| | ||||| || | | || ||||||||||||||| | ||||| ||||||| ||||| || || ||| ||||||||||||| |
ttgatgatgaaaatatggtcgatattcgtcttttgtttatcaagtatggtcagagtattagtgatgtacttgttactgaacactatcctgtgtgtgac--------agGGTTACGTGGTGTATCGCGTCCGCGTACGCCGCGGGGGTAGGAAGAGGCCTGTTGCCAAGGGTATTGTGTATGGAAAACCTAAGAACCAGGGTATCACAC
upper sequence: GRMZM2G302876_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ27946 (Selaginella moellendorffii), 3'ss of exon 2
attaggagtcttgagggtacccctaattatggtccccgacaagtttgagtacctatgtcatgattttatttgatg-ttgtgttgtggtaattcatctttagGGTTATGTTATGTACCTTGTCCGTGTGAGGCATGGTGGTAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC
| || ||| | || | | || | || | ||| | |||| || ||| | |||| |||||||||| | | || || | |||||||| | ||||| | ||||||||||| ||||||||| |||||||||||||||
-------------------------------------gtaaaatttctcctttcttcgtgtgtgctagctctttgatcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTCTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
upper sequence: GRMZM2G302876_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
attaggagtcttgagggtacccctaattatggtccccgacaagtttgagtacctatgtcatgattttatttgatg-ttgtgttgtggtaattcatctttagGGTTATGTTATGTACCTTGTCCGTGTGAGGCATGGTGGTAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC
| || ||| | || | | || | || | ||| | |||| || ||| | |||| |||||||||| | | || || | |||||||| | ||||| | ||||||||||| ||||||||| |||||||||||||||
-------------------------------------gtaaaatttctcctttcttcgtgtgtgctagctctttgatcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagtacctatgtcatgattttatttgatgttgtgttgtggtaattcatctttagGGTTATGTTATGTACCTTGTCCGTGTGAGGCATGGTGGTAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC
atttgat putative branch site (score: 5)
ttcatcttt putative PPT
atgattttatttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attaggagtcttgagggtacccctaattatggtccccgacaagtttgagtacctatgtcatgattttatttgatgttgtgttgtggtaattcatctttagGGTTATGTTATGTACCTTGTCCGTGTGAGGCATGGTGGTAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttg