Sequence
atgc intronic sequence ATGC exonic sequence...tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 4
----tgggtgcattt---tttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatga-ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
| | || || ||| | || ||| || | ||||| |||| | | | | |||| ||| ||| || || |||| | || | ||||||||||||||| ||||| |||||||||||||| ||||||||||| || || ||||||||||| || ||||||||||| |||||||| ||||| ||||||||
aagattagcacaattgggtttgcagacccaaatgtgttgcctaccatttcttgt----tatacctattgt----tcttacagaagcctgctgggcaacttttgtgcagGGAAAACTGTTTTTACCAGTGATCATGCACTAAAACTTGAGTCTGTCCCGGACTGGATAGCAATCGTTGGAAGTGGATACATTGGGCTTGAATTCAGTGA
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 4
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
||| | || || | || || | ||| | |||||| | | ||| ||| | | ||| || | | | || |||| || ||||| |||| ||||| |||||||| ||||| ||| | ||||| || |||||||| ||||| ||||||||||| ||||| ||||| ||||||||
ggggatctttgttcactgatactgtccctcttgtttttctgttttgttatttcttcttcttggtatcattaatgaaagctcaccaagtaaatgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGA
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
|| | ||| || || || | || | | ||| | || |||| || | | || | ||| || | ||||| || ||||| | || ||||| ||||| ||||| | ||||| || || || ||||| || ||||| ||||||||||| ||||| ||||||||||||||
---gtacgtttcttgttttgg-acgtagagttgttaagggagcatgcagactt---------gattattccttgaatgtttacattttggcgct--gcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
| || | | | | || || | | | | || | | |||| | | | | || | | || |||| || | |||||| || ||||| | || |||||||||||| ||||| | ||||| ||||| |||||||| || || || ||||||||||| || || ||||||||||||||
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaaaccaaagcttctcatttcttttagtatagcaagtaccc-taatattcc-tcatattttgtgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0060g01410.t01 (Vitis vinifera), 3'ss of exon 3
tgggtgcattttttat-tgtgacatgtgtatta-gttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
| | || | || || | ||| || || ||| | | | | || | | || || || | | | | | |||||||||||||||| | || |||||||| ||||| ||| | || | |||| || |||||||| |||||||| ||||| |||||||| |||||||| |||||
-gaaaaccttgaaagtgcctgttatcttcattttattcacttttgcatggaaatctgctattccctcaggattactaattttt-tcaggtagtggtctgcagGGAAAACTGTAATAACCAGTGATCAAGCACTTAAATTGGAATTTATTCCTGATTGGATAGCCATTGTTGGCAGTGGCTACATTGGTCTTGAGTTTAGTGA
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 4
tgggtgcattttttat-tgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
| || | || || | ||| | |||| || | | | || | |||| | | | | | |||||||||||||||| | || |||||||| ||||| ||| | || | ||||| || |||||||| |||||||| ||||| |||||||| |||||||| |||||
-aaaaaccttgaaagtgcctgttatcttcattttattcacttttgcatggaaatctgctattccctcaggatgactaattttttcaggtagtggtctgcagGGAAAACTGTAATAACCAGTGATCAAGCACTTAAATTGGAATTTGTTCCCGATTGGATAGCCATTGTTGGCAGTGGCTACATTGGTCTTGAGTTTAGTGA
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 4
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattcta----ctggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
| | | | || || | || | | | | || || ||| | ||| | | ||| ||| | | ||||| | ||| || | ||||||||| ||||| |||| || |||||||| || ||||| ||||| ||||| || |||||||| ||||| ||||||||||| ||||| ||||| ||||||||
---ttccttgtattccagttatctgcaaaatctataatatgaatt-tgtcaatcttttggtttttgtgttcaaagatttctaatcaccagataatgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGA
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 4
-tgggtgcattttttat-tgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
|| ||| | || ||| | ||| | || || | | ||| | ||| || | | || | || |||| ||||| || || || ||||| |||||||| || |||| | |||| ||||||||||||| || || ||||| || ||||||||||| || |||||||||||
taggaaaaattatgtaggtgttgcccatgttctgaacgatatagctgcagcactgtttttgaagtgaacttgatgcttactcaaaaacctggttat--gcagGAAAGACCGTTTTTACAAGTGATCACGCTTTGAAGTTAGAGTGGATTCCAGACTGGATTGCGATCGTTGGCAGCGGTTACATTGGTCTAGAGTTCAGTGA
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttg-ttgtatgttctcacaaaattctactgga-tgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
|| | | || || ||| |||| | ||| || || | | | ||||| | | | | || | ||| |||| || || || || || || |||||||| ||||| || |||| | ||||||||||| || ||||||||||||||||||||||| ||||||||||| ||
---gta-agaagtcatggtcgttggtggattaaaatgcttttaaagtttatgctggtcgattgtaaaaatgattatctcttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 4
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactgg-atg-attatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
| | | | | || || | || || | || ||| ||| ||| | | ||||||| | | ||| | || |||| || || || || || ||||| ||||| |||| || |||| |||| |||||||| ||||||| ||||||||||||||||| ||||||||||||||
-gtaagaaactatcatcgt--------tgatactttagatgctttcaaatcttgtattgccgcg-ataagaacaaaatctgattcatatggaggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
ttctcac putative branch site (score: 2)
atgattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- -gtgcatt
- - - - - - - - - - -catgtgt
- - - - - - - - - - - - - - - - - tgacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggatg