Sequence
atgc intronic sequence ATGC exonic sequence...ttgcattggttgctagcagtcgcagagttgaattgatggcaattcgttaatcgttatggtgatgatgctgtttatttttgcatgcttgcgtgtgcattagGTCTAGAGAGGTGTGGGAAGAGCTGCAGGCTGAGGTGGATCAACTACCTCAGGCCGGACCTCAAGAGGGGAGCGTTCTCGCAGGAAGAGGAGGACCTCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G150841_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g44090.3 (Oryza sativa), 3'ss of exon 1
ttgcattggttgctagcagtcgcagagttgaattgatggcaattcgttaatcgtt--atggtgatg-atgctgtttatttttgcatgcttgcgtgtgcattagGTCTAGAGAGGTGTGGGAAGAGCTGCAGGCTGAGGTGGATCAACTACCTCAGGCCGGACCTCAAGAGGGGAGCGTTCTCGCAGGAAGAGGAGGACCTCAT
|| | ||| ||| | | | | | | | |||| || | ||| | |||| || || || || ||| | ||||||||| || ||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||| ||||| |||||||| || ||||||||
ttaactgaattg--agctgaaatgaacctttttaggtaggaattaattggtagtttgaatttgatatatatcattagaaattcca-atttgtggttgcattagGCCTTGAGAGATGTGGGAAGAGCTGCAGGCTGAGGTGGATAAACTACCTCAGGCCAGACCTCAAGAGGGGAGCATTCTCACAGGAAGAAGAAGACCTCAT
upper sequence: GRMZM2G150841_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g44090.2 (Oryza sativa), 3'ss of exon 1
--------------------ttgcattggttg---ctagcagtcgcagagttgaattgatggcaattcgttaatcgtt--atggtgatg-atgctgtttatttttgcatgcttgcgtgtgcattagGTCTAGAGAGGTGTGGGAAGAGCTGCAGGCTGAGGTGGATCAACTACCTCAGGCCGGACCTCAAGAGGGGAGCGTTCTCGCAGGAAGAGGAGGACCTCAT
| ||| || ||| | | | | | | | |||| || | ||| | |||| || || || || ||| | ||||||||| || ||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||| |
attacgaaattttcatgtcacttaattaactgaattgagctgaaatgaacctttttaggtaggaattaattggtagtttgaatttgatatatatcattagAAATTCCA-ATTTGTGGTTGCATTAGGCCTTGAGAGATGTGGGAAGAGCTGCAGGCTGAGGTGGATAAACTACCTCAGGCCAGACCTCAAGAGGGGAGCAT-------------------------
upper sequence: GRMZM2G150841_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 1
--ttgcattggttgctagcagtcgcagagttgaattgatggcaattcgttaatcgttatggtgatgatgctgtttatttttgcatgcttgcgtgtgcattagGTCTAGAGAGGTGTGGGAAGAGCTGCAGGCTGAGGTGGATCAACTACCTCAGGCCGGACCTCAAGAGGGGAGCGTTCTCGCAGGAAGAGGAGGACCTCAT
||| | | | | || | |||||| | ||||||| ||| || || || | || || | | |||| |||||| | ||||| ||||||||||||||| || ||||||||||||||||| ||||||| | || | || | || ||| | ||||||| || | ||
taacatatttaaagtgaaaaaaggttcttttca-ttgatgtaaggaatctaatcgt-gtggagaaattgatgaatgttcctggacaatgaatgctgcaacagGTCTCCAAAGGTGCGGGAAGAGCTGCAGGTTGCGGTGGATCAACTACCTCCGGCCGGATTTGAAACGAGGCGTATTTTCGGCAGCAGAGGAGAACTTGAT
upper sequence: GRMZM2G150841_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 1
--ttgcattggttgctagcagtcgcagagttgaattgatggcaattcgttaatcgttatggtgatgatgctgtttatttttgcatgcttgcgtgtgcattagGTCTAGAGAGGTGTGGGAAGAGCTGCAGGCTGAGGTGGATCAACTACCTCAGGCCGGACCTCAAGAGGGGAGCGTTCTCGCAGGAAGAGGAGGACCTCAT
| | ||||| | | |||| | | ||| | | || | | | | | | |||| || || | |||| |||||| | |||||||||||||||||||||||| | |||||||||||| | || || || | || | || | ||||| | ||| || | ||
aatgaaaatggtttcgcaggaatgaagagcgaccaggttagcacactttgttttgtactaatcactaaccaat--atttgtgtttgtgaatggatgcaacagGTCTTCAAAGGTGTGGGAAGAGCTGCAGGCTGCGATGGATCAACTACTTGAGACCAGATTTGAAACGAGGGGTATTCTCCGCGACAGAAGAAAGTTTGAT
upper sequence: GRMZM2G150841_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
ttgcattggttgctagcagtcgcagagttgaattgatggcaattcgttaatcgttatggtgatgatgctgtttatttttgcatgcttgcgtgtgcattagGTCTAGAGAGGTGTGGGAAGAGCTGCAGGCTGAGGTGGATCAACTACCTCAGGCCGGACCTCAAGAGGGGAGCGTTCTCGCAGGAAGAGGAGGACCTCAT
|| ||| || || | | | | | | | | || | || | || ||| || | || ||||||||||||||||||||||| ||||||||||| ||| |||| ||| | || ||||| || ||||| | || || || | ||
-----------------------------------gtgagtatttgtacctcaatttcaagttctcgtgagctcacaattcttggtggcat-tgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttaatcgttatggtgatgatgctgtttatttttgcatgcttgcgtgtgcattagGTCTAGAGAGGTGTGGGAAGAGCTGCAGGCTGAGGTGGATCAACTACCTCAGGCCGGACCTCAAGAGGGGAGCGTTCTCGCAGGAAGAGGAGGACCTCAT
cgttaat putative branch site (score: 4)
tgtttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcattggttgctagcagtcgcagagttgaattgatggcaattcgttaatcgttatggtgatgatgctgtttatttttgcatgcttgcgtgtgcattagGTCTAGAGAGGTGTGGGAAGAGCTGCAGGCTGAGGTGGATCAACTACCTCAGGCCGGACCTCAAGAGGGGAGCGTTCTCGCAGGAAGAGGAGGACCTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA