Sequence
atgc intronic sequence ATGC exonic sequence...tgtacgactaatccttgatagttgacatttctaatcagttttttttttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G116840_T06 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
--tgtacgactaatccttgatagttgacatttctaatcagttttttttttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT
|| | | | | | | ||| | | | | || || || | | | || || | || || || | ||||| || |||||||| |||||||||||||||| || |||||||| || |||||| | |||||||| || || || ||| |||| ||||| |||| ||||
tgggttctggaatttttgtccacctaccatctttgtttaacaattaacatgtcaatttgaccgcagata-tattgtttactg-ttgtttcacttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG-----------
upper sequence: GRMZM2G116840_T06 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G07810.2 (Glycine max), 3'ss of exon 4
tgtacgactaatccttgatagttgacattt---ctaatcagttttttttttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT
| || || || | |||| || || || ||| | | ||| | | || || || | | |||||||| ||||||| || ||||| || |||||||| || ||||||||||| ||||| || | || ||||| || ||||| | ||||||
---gttagccatttttttctttttaaatttagatgaaagcgtgattgacttggtactggtttttgatggtgagctgacatttaatgtgcttggcatcatgcagATATATTGTATGATTCATGGTCTCCGGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGGT---------
upper sequence: GRMZM2G116840_T06 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G07810.1 (Glycine max), 3'ss of exon 4
tgtacgactaatccttgatagttgacattt---ctaatcagttttttttttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT
| || || || | |||| || || || ||| | | ||| | | || || || | | |||||||| ||||||| || ||||| || |||||||| || ||||||||||| ||||| || | || ||||| || ||||| | ||||
---gttagccatttttttctttttaaatttagatgaaagcgtgattgacttggtactggtttttgatggtgagctgacatttaatgtgcttggcatcatgcagATATATTGTATGATTCATGGTCTCCGGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG-----------
upper sequence: GRMZM2G116840_T06 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 4
tgtacgactaatccttgatagttgacatttctaatcagttttttt--tttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT
|| || | | || | || | || | || | || ||| | | | | | | || ||||| | | |||||||| ||||||| || |||||||| |||||||| || ||||||||||| ||||| || | || ||||| || ||||| | ||||
-gt-taaccatttttttctttttaaatttagataaaagcatgattgacttggtgttggtttttggtggtgagctgacatttgatgtgcttgacatcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG-----------
upper sequence: GRMZM2G116840_T06 (Zea mays), 3'ss of exon 3
lower sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
-tgtacgacta-atccttgatagttgacatttctaatcagttttttttttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT
| | | || |||| | || | | | || || || ||| ||| | | |||| || || || | | | ||||||| ||||||| |||||||| ||||| ||||| || ||||||||||| || ||||| | || ||||| || |||||| | ||||||
ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctggaaga-agtatctgatg-ttgtgtatcatcgttgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG-----------
upper sequence: GRMZM2G116840_T06 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g13180.t01 (Vitis vinifera), 3'ss of exon 4
----tgtacgactaatccttgatagttgacatttctaatcagttttttttttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT
|| | | || | || | | | | || || || || |||| || | |||| || | | | | || | |||||||| || ||||| || ||||||||||| ||||| || ||||| ||||||||||||||| | || ||| | || ||||| | | |||
ggttcttatttcaatcccattattttatcaactgattctctgtggttgattgtccatcaacacactgacatctaatatca--tagcttatttgttttc--acagATATTCTATATGATTCATGGTCCCCAGCCATGACAGTTAGTTCAATCTGTATCAGCATACTCTCCATGTTATCGAGCTCAACTGTGAAG-----------
upper sequence: GRMZM2G116840_T06 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 4
------tgtacgactaatccttgatagttgacatttctaatcagttttttttttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT
| | | || | || || ||||| | | || | | | ||| || ||| || || |||||| || | | | | ||||||| ||||||| || ||||||||||| ||||| || ||||||||||| |||||||| | || ||||| || ||||| | | |||
tttatggatccaaatatgttagtttgattatgatgtctaa--aactaacttatgtacctttcaatctgaaatttta-tatttattgactcatg---tgatgtgcagATATTTTGTATGATTCTTGGTCCCCAGCCATGACAGTTAGTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAG-----------
upper sequence: GRMZM2G116840_T06 (Zea mays), 3'ss of exon 3
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
tgtacgactaatc--cttgatagttgacatttctaatcagttttttttttgccatgaaaatgggatatt-ctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT
|||| | | ||| | || ||| | || ||| | | || ||| | || | | | | | | ||||||| || |||||||| ||||| ||||| ||||| || ||||||||||| |||||||| | || ||| |||| || || | | |||
---acgagttcccaacttaacgaaaactatctctgtgtacttgaatttaacatgttgcgtttaattaagactaatttctgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG----------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT
ttcctccacttacct CT-rich tract
atgaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtacgactaatccttgatagttgacatttctaatcagttttttttttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - tgacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccac