Sequence
atgc intronic sequence ATGC exonic sequence...catagtttatctcttacgagacatgtaatgtgtctttacactatcatgctttgaccctcttgattccaatacatctgctaacaaaaattattgagtgcagGTTATTGATTTTCATCAGACAGTAGAAGTCAATGGTATTAGATTCTGGTGTTATACTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
Basic information
| species | Glycine max |
| transcript | GLYMA12G29040.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G29040.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g63590.1 (Oryza sativa), 3'ss of exon 4
----catagtttatctcttacgagacatgtaatgtgtctttacactatcatgctttgaccctcttgattccaatacatctgctaacaaaaattattgagtgcagGTTATTGATTTTCATCAGACAGTAGAAGTCAATGGTATTAGATTCTGGTGTTATACTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
|||| ||| | | | ||| ||| | || ||| || ||| | ||||| | || ||||| ||| || ||||||| || || || || |||||| | ||||| ||||| || | |||||||| |||||||| |||||||| ||||| ||||| ||||||||||| ||||| |
tccatatagcatattgttgattcttcttgtgatga--tcgaaagcttgtatgtatttcatggagtgaatg-aatacttttgttaacataaaa-atgccttgcagGTCATAGACTTCCACCAGACATTGGAAGTTAATGGCATACGCTTCTGGTGCTATACTGCTGGCCATGTACTTGGCGCTGCAATGTTCATGGTGGACATTG
upper sequence: GLYMA12G29040.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G422649_T01 (Zea mays), 3'ss of exon 4
---catagtttatctcttacgagacatgtaatgtgtctttacactatcatgctttgaccctcttgattccaatacatctgctaa--caaaaattattgagtgcagGTTATTGATTTTCATCAGACAGTAGAAGTCAATGGTATTAGATTCTGGTGTTATACTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
| || || | | | |||| || | | | | ||| | | || | | | | | ||| ||| | | |||||||||||||||| || |||||| | ||||| ||||| || | |||||||| || ||||| |||||||| |||||||| || |||||||||||||| || |
ctttaaagcaaatgcaggattctgctcatcatgt---ttgaaattgagaggctatttttcagggaatac--acatttttattaatctgaaagtcgtcttctgcagGTTATTGATTTCCACCAGACATTGGAAGTTAATGGGATACGCTTCTGGTGCTACACTGCTGGCCATGTGCTTGGTGCCGCCATGTTCATGGTTGATATTG
upper sequence: GLYMA12G29040.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G083346_T01 (Zea mays), 3'ss of exon 4
catagtttatctcttacgagacatgtaatgtgtctttacactatcatgctttgaccctcttgattccaatacatctgctaa--caaaaattattgagtgcagGTTATTGATTTTCATCAGACAGTAGAAGTCAATGGTATTAGATTCTGGTGTTATACTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
|| |||| | | || |||| | | || | || | | | | | ||| ||| || | ||||||||||| ||||| || ||||| | ||||| ||||| || | |||||||| || ||||| |||||||| |||||||| |||||||||||||| || || |
--tactttaaagaaaatgcagaattctgctcatcttgtttgaaagagactatttttttcagggaatgcacatttttattaatctgaaagttgtcttgtgcagGTTATAGATTTCCACCAGACGTTGGAAGTTAATGGGATACGCTTCTGGTGCTACACTGCTGGCCATGTACTTGGTGCCGCTATGTTCATGGTGGATATTG
upper sequence: GLYMA12G29040.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0035g00170.t01 (Vitis vinifera), 3'ss of exon 4
-catagtttatctcttacgagacatgtaatgtgtctttacactatcatgctttgaccct-cttgattccaatacatctgctaacaaaaattattgagtgcagGTTATTGATTTTCATCAGACAGTAGAAGTCAATGGTATTAGATTCTGGTGTTATACTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
|| || | |||| | | || | | | | | | | || | | | | || || | | ||| ||| ||| | |||||||||||||||| ||||| || ||||||| |||||||| ||| |||||||| || | |||||||||||| ||||||| ||||| |||||||| || |
gaatgtttggccatttacaaaaattg-acttaaggtatgtagtttaattttatcatctcatttaatcttcctgtaactg-taattaaatctcccttctgcagGTTATTGATTTCCATCAAACTTTAGAAGTAAATGGTATACAATTTTGGTGTTACACAACTGGCCATGTCCTTAGTGCTGCCATGTTTATGGTTGATATTG
upper sequence: GLYMA12G29040.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0035g00030.t01 (Vitis vinifera), 3'ss of exon 4
-catagtttatctcttacgagacatgtaatgtgtctttacactatcatgct-ttgaccctcttgattccaatacatctgctaacaaaaattattgagtgcagGTTATTGATTTTCATCAGACAGTAGAAGTCAATGGTATTAGATTCTGGTGTTATACTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
|| | | |||| | | || | | | | | | | || | || | | || || | | ||| ||| ||| | |||||||||||||||| |||||||| ||||||| |||||||| |||| |||||||| || || ||||| |||||||||||||| ||||| |||||||| || |
gaatgttgggccatttacaacaattg-actttagatatgtagcttaattttattatctcatttaatcttcctgtaactg-taattaaatctcccttctgcagGTTATTGATTTCCATCAGACTTTAGAAGTAAATGGTATACGATTTTGGTGTTACACAGCTGGCCACGTCCTTGGTGCTGCCATGTTTATGGTTGATATTG
upper sequence: GLYMA12G29040.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0035g00190.t01 (Vitis vinifera), 3'ss of exon 4
-catagtttatctcttacgagacatgtaatgtgtctttacactatcatgctttgaccct-cttgattccaatacatctgctaacaaaaattattgagtgcagGTTATTGATTTTCATCAGACAGTAGAAGTCAATGGTATTAGATTCTGGTGTTATACTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
|| || | ||| | | || | | | | | | || | | | | || || | | ||| ||| ||| | |||||||||||||||| |||||||| ||||||| ||||| || |||| ||||||||||| || ||||| |||||||||||||| ||||| |||||||| || |
gaatgtttggccatttataacaattg-acttcagatatgtagcttaattttatcatctcatttaatcttcctgtaactg-taattaaatctcccttctgcagGTTATTGATTTCCATCAGACTTTAGAAGTAAATGGCATACGATTTTGGTGTTATACAGCTGGCCACGTCCTTGGTGCTGCCATGTTTATGGTTGATATTG
upper sequence: GLYMA12G29040.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S23_196V6.1 (Physcomitrella patens), 3'ss of exon 4
catagtttatct-cttacgagacatgtaatgtgtctttacactatcatgctttgaccctcttg-attccaatacatctgctaacaaaaattattgagtgcagGTTATTGATTTTCATCAGACAGTAGAAGTCAATGGTATTAGATTCTGGTGTTATACTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
|| | | |||| ||| | || ||| || | | || || | ||| | | | | | | | | || ||| ||||| |||||||||||||| || | ||||||||||| ||| |||||||||||||||| ||||||||||| | ||||| || ||||||||||| |||||||
-atgatgaggttatttactagattattgatatgtacttcctaaaaca-gcggcatcgtgtttgcaattaagcggttgtataaccctatgttggtgatgacagGTGATTGATTTTCATCAAACTATGGAAGTCAATGGGATTCGATTCTGGTGTTATACAGCAGGCCATGTATTGGGTGCAGCCATGTTCATGGTAGACATAG
upper sequence: GLYMA12G29040.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S77_275V6.1 (Physcomitrella patens), 3'ss of exon 5
catagtt-tatctcttacgagacatg-taatgtgtctttacactatcatgctttgaccctcttgattccaatacatctgctaacaaaaattattgagt--gcagGTTATTGATTTTCATCAGACAGTAGAAGTCAATGGTATTAGATTCTGGTGTTATACTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
| || | | |||| | ||||| || ||| | | | | | | | || ||| | || ||| | ||| | | || |||||| |||||||||||||| || | ||||| ||||| ||| | |||||||||||||| ||||||||||| | ||||| ||||||||||||||||| ||||
tgtgtttgtgttatttacta-acatgctagtgtaaact-atttgaatgagttgtatcgtactctatttggg--cgattgttaaactatattttcgtgttggcagGTGATTGATTTTCATCAAACCATGGAAGTAAATGGGATTCGGTTCTGGTGTTATACAGCAGGCCATGTATTGGGTGCAGCTATGTTCATGGTTGATATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgctttgaccctcttgattccaatacatctgctaacaaaaattattgagtgcagGTTATTGATTTTCATCAGACAGTAGAAGTCAATGGTATTAGATTCTGGTGTTATACTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
tgctaac putative branch site (score: 1)
taacaaaaattattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catagtttatctcttacgagacatgtaatgtgtctttacactatcatgctttgaccctcttgattccaatacatctgctaacaaaaattattgagtgcagGTTATTGATTTTCATCAGACAGTAGAAGTCAATGGTATTAGATTCTGGTGTTATACTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - -catgtaa
- - - - - - - - - - - - - - -gtgtctt
- - - - - - - - - - - - - - - - - - - - - -tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa
