Sequence
atgc intronic sequence ATGC exonic sequence...catttagatttacttcaagaaatctgctcaacttatcttaaaaaaatttatgttgtttgagagatggttttgtgacatagtaaattgtcgtggttatcagGTGGATATGATAAGGAAGAAAAGGCCGCGAGAGCTTATGATTTGGCAGCTCTAAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
Basic information
species | Glycine max |
transcript | GLYMA01G02760.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G02760.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G10510.2 (Arabidopsis thaliana), 3'ss of exon 3
catttagatt-tacttcaagaaatctgctcaacttatcttaaaaaaatttatgttgtttgagagatggttttgtgacatagtaaattgtcgtggttatcagGTGGATATGATAAGGAAGAAAAGGCCGCGAGAGCTTATGATTTGGCAGCTCTAAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
|| | | | ||||| || | |||| | || | | | | | ||| | |||| | | |||| | | |||||||||||||| || ||||| ||||| || ||||||| ||||| |||||||| || |||||| | | |||||||||||||| ||||||
aatcaacagtatacttgggtaagaacaaatatcttaatcagtcagcatgtgaataatgttgaatatgtatctgtggtgtctaactttgttaatgat-tcagGTGGATATGACAAAGAAGATAAGGCAGCTCGAGCTTACGATTTAGCAGCTCTGAAATACTGGAATGCTACTGCTACCACCAATTTCCCT
upper sequence: GLYMA01G02760.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G10510.1 (Arabidopsis thaliana), 3'ss of exon 4
catttagatttacttcaagaaatctgctcaacttatcttaaaaaaatttatgttgtttgagagatggttttgtgacatagtaaattgtcgtggttatcagGTGGATATGATAAGGAAGAAAAGGCCGCGAGAGCTTATGATTTGGCAGCTCTAAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
|| |||| | || || || | | | |||||| | ||| | |||| | | |||| | | |||||||||||||| || ||||| ||||| || ||||||| ||||| |||||||| || |||||| | | |||||||||||||| ||||||
-----------gtaagaacaaatat-cttaatcagtcagcatgtgaataatgttg-----aatatgtatctgtggtgtctaactttgttaatgat-tcagGTGGATATGACAAAGAAGATAAGGCAGCTCGAGCTTACGATTTAGCAGCTCTGAAATACTGGAATGCTACTGCTACCACCAATTTCCCT
upper sequence: GLYMA01G02760.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G10510.3 (Arabidopsis thaliana), 3'ss of exon 4
catttagatttacttcaagaaatctgctcaacttatcttaaaaaaatttatgttgtttgagagatggttttgtgacatagtaaattgtcgtggttatcagGTGGATATGATAAGGAAGAAAAGGCCGCGAGAGCTTATGATTTGGCAGCTCTAAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
| ||||| || | |||| | || | | | | | ||| | |||| | | |||| | | |||||||||||||| || ||||| ||||| || ||||||| ||||| |||||||| || |||||| | | |||||||||||||| ||||||
-------gtatacttgggtaagaacaaatatcttaatcagtcagcatgtgaataatgttgaatatgtatctgtggtgtctaactttgttaatgat-tcagGTGGATATGACAAAGAAGATAAGGCAGCTCGAGCTTACGATTTAGCAGCTCTGAAATACTGGAATGCTACTGCTACCACCAATTTCCCT
upper sequence: GLYMA01G02760.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 4
catttagatttacttcaagaaatctgctcaacttatcttaaaaaaatttatgttgtttgagagatggttttgtgacatagtaaattgtcgtggttatcagGTGGATATGATAAGGAAGAAAAGGCCGCGAGAGCTTATGATTTGGCAGCTCTAAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
|| | | | || | || | ||| | || | | | |||| ||| | | | | | | |||||||||||| |||||||| | || || ||||| ||||| ||||||||| |||| ||||||||| | |||||||| || || || ||
-----------------gtaagcaagataatattctattgacaaattaattgatatatcgagtatggcaa-atgatgt--ccatctttgattaattcaagGTGGATATGACAAGGAAGATAGAGCAGCTAGAGCCTATGACTTGGCAGCTTTAAAATACTGGGGTTCTACTGCTACTACAAATTTTCCG
upper sequence: GLYMA01G02760.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s1291g00010.t01 (Vitis vinifera), 3'ss of exon 3
-------catttagatttacttcaagaaatctgctcaacttatcttaaaaaaatttatgttgtttgagagatggttttgtgacatagtaaattgtcgtggttatcagGTGGATATGATAAGGAAGAAAAGGCCGCGAGAGCTTATGATTTGGCAGCTCTAAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
| || | || ||||| || | | || || | ||| || | | | | || || || | | |||| ||||||||||| ||||| |||||||||||||| || || || |||||||| ||||||||||||||||||||| | |||| || ||||| ||||||
cgttcgcttcctttgttctttctaacaaatcctctaatactgggttgaacagtattacagagtatta-aattaattatg----atgg--acttgtgtaaattatcagGTGGGTATGACAAGGAAGAAAAGGCAGCAAGGGCCTATGATTTAGCAGCTCTAAAGTACTGGGGTGCTTCTGCAACTACCAATTTCCCT
upper sequence: GLYMA01G02760.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------------------------------catttagat--ttacttcaagaaatctgctcaacttatcttaaaaaaatttatgttgtttgagagatggttttgtgacatagtaaattgtcgtg----gttatcagGTGGATATGATAAGGAAGAAAAGGCCGCGAGAGCTTATGATTTGGCAGCTCTAAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
|| ||| | | | || || | || | | | || | || || | || || | || | | | | ||| ||||||||||| ||||||||||| || ||||| || || |||||||| || || ||||||||||||| | |||| |||||| ||
gtatgactggagggacttgaagcacagaaccctctccatgtgcttccttctgagccgttgtgaagttcaaagaacagtctgctgaaagtttgagctagaacagtcattggatgatcaggcgatgattgctatgtggtgaaggttgtatacgca-gcatctcacgatctaatgtgtttgggcactgtcacgtgctgcgcagTATACTTAGGAGGATATGATAAAGAAGAAAAGGCAGCCAGAGCCTACGACTTGGCAGCGCTCAAATACTGGGGTCCCAGCACCACCATCAACTTTCCG
upper sequence: GLYMA01G02760.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 1
------------------------------------------------------------------------------------------------catttagatt-tacttcaagaaatctgctcaacttatcttaaaaaaatttatgttgtttg-agagatggttttgtgacatagtaaattgtcgtggttatcagGTGGATATGATAAGGAAGAAAAGGCCGCGAGAGCTTATGATTTGGCAGCTCTAAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
| || | || || | | | | |||| | ||||| | | | ||| ||| | || || | ||| ||| | ||| ||||||||| ||| || ||||| || |||||||| ||| |||||||||| ||||||||||| || || | || || ||||| ||
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggtgtggtacttgatccatcctccagtgtacttaggtgagtaatct--atcgaatttttctcgattgtggagctaaacttttggtggttttctttg-cgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttatgttgtttgagagatggttttgtgacatagtaaattgtcgtggttatcagGTGGATATGATAAGGAAGAAAAGGCCGCGAGAGCTTATGATTTGGCAGCTCTAAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
atagtaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catttagatttacttcaagaaatctgctcaacttatcttaaaaaaatttatgttgtttgagagatggttttgtgacatagtaaattgtcgtggttatcagGTGGATATGATAAGGAAGAAAAGGCCGCGAGAGCTTATGATTTGGCAGCTCTAAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - cttcaag
- - - - - - - - - - - -ctgctca
- - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatggtt