>retro_sscr_479
ATGGCAGCCTCGAAGAAAGCTGTTTTGGGGCCGTTGGTGGGAGCAGTGGACCAGGGCACCAGCTCGACGCGCTTTTTGGT
TTTCAATTCAAAAACAGCCGAACTACTTAGTCATCATCAAGTGGAAATAGAACAAAAATTTCCAAAAGAAGGGTGGGTGG
AACAAGACCCTAAGGAAATCCTGCAGTCCGTCTATGAGTGTATAGAGAAAACGTGTGAGAAACTTGGTCAGCTCAATATT
GATATTTCCAACATAAAAGCTATTGGTGTCAGTAACCAGAGGGAAACCACTGTGGTCTGGGACAAGTTAACTGGAGAACC
CCTCTACAATGCTGTGGTGTGGCTTGATCTAAGAACCCAGTCTACCGTTGCGAACCTTAGTAAAATCATTCCAGTGAATA
ATAACTTTGTCAAGACCAAGACAGGCCTTCCACTCAGCACGTACTTCAGTGCAGTGAAGCTTCGTTGGCTCCTTGATAAT
GTGAGAAAAATTCAAAAGGCAGTTGAAGAAGATAGAGCTCTTTTTGGGACCATTGATTCCTGGCTTATTTGGAGCTTGAC
AGGAGGAGCCAGGGGAGGTGTTCATTGTACAGACGTAACAAATGCAAGTAGGACGATGCTATTCAACATTCATTCTTTGG
AATGGGATAAAGAGCTCTGTGAATTTTTTGAAGTTCCAATGAAAATTCTGCCAAACGTCCGGAGTTCTTCTGAGATCTAT
GGCCTAATGAAAGCTGGGGCCTTGGAAGGCGTGCCAATATCTGGGTGTTTGGGAGACCAGTCTGCTGCATTGGTGGGACA
GATGTGCTTCCAGGATGGACAGGCCAAAAACACGTATGGAACAGGCTGTTTCTTACTATGTAATACAGGCCACAAGTGTG
TGTTTTCTGAACATGGCCTTCTGACCACAGTGGCTTACAAACTTGGCAGAGACAAACCAGTGTATTATGCATTAGAAGGC
TCAGTAGCTATAGCTGGTGCTGTTGTTCGCTGGCTAAGAGACAATCTTGGAATTATAAAGACCTCAGAGGAAATTGAAAA
ACTTGCTAAAGAAGTAGGTACTTCTTATGGCTGTTATTTTGTCCCAGCCTTTTCAGGGCTATATGCACCTTACTGGGAGC
CCAGTGCAAGAGGGATCATCTGTGGGCTCACTCAATTCACCAATAAATGCCATATTGCTTTTGCTGCGTTAGAAGCTGTT
TGTTTCCAAACCCGAGAGATTTTGGATGCCATGAACCGTGACTGTGGAATTCCACTCAGCCATTTGCAGGTAGATGGGGG
AATGACCAACAACAAAATTCTTATGCAGCTACAAGCAGACATTCTGTATATCCCAGTAGTGAAGCCCTCAATGCCAGAAA
CAACCGCCTTGGGAGCTGCCATGGCAGCAGGGGCTGCAGAAGGAGTTGGCGTTTGGAGTCTCAAACCTGAGGATTTATCA
GCTGTCACGATGGAGCGGTTTGAACCTCAGATCAATGCTAAAGAAAGTGAAATTCGTTATTCCACATGGAAGAAAGCTGT
GAAGAAGTCCATGGGTTGGGTTACAACTCAGTATCCAGAAAATGGTGACCCT
ORF - retro_sscr_479 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
94.66 % |
Parental protein coverage: |
100. % |
Number of stop codons detected: |
0 |
Number of frameshifts detected |
0 |
Retrocopy - Parental Gene Alignment:
Parental | MAAANKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVELKQEFPKEGWVEQDPKEILNSVYECIEK |
| MAA..KAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVE..Q.FPKEGWVEQDPKEIL.SVYECIEK |
Retrocopy | MAASKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIEQKFPKEGWVEQDPKEILQSVYECIEK |
|
Parental | TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVENLSKRIPGNNNFVKSK |
| TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTV.NLSK.IP.NNNFVK.K |
Retrocopy | TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVANLSKIIPVNNNFVKTK |
|
Parental | TGLPLSTYFSAVKLRWLLDNVRKVQKAVEEERALFGTVDSWLIWCLTGGANGGVHCTDVTNASRTMLFNI |
| TGLPLSTYFSAVKLRWLLDNVRK.QKAVEE.RALFGT.DSWLIW.LTGGA.GGVHCTDVTNASRTMLFNI |
Retrocopy | TGLPLSTYFSAVKLRWLLDNVRKIQKAVEEDRALFGTIDSWLIWSLTGGARGGVHCTDVTNASRTMLFNI |
|
Parental | HSLEWDKELCEFFEIPMKILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG |
| HSLEWDKELCEFFE.PMKILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG |
Retrocopy | HSLEWDKELCEFFEVPMKILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG |
|
Parental | TGCFLLCNTGRKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVVRWLRDNLGIIKTSEEIEKLAK |
| TGCFLLCNTG.KCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVVRWLRDNLGIIKTSEEIEKLAK |
Retrocopy | TGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVVRWLRDNLGIIKTSEEIEKLAK |
|
Parental | EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNRCHIAFAALEAVCFQTREILDAMNRDCGMPLR |
| EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTN.CHIAFAALEAVCFQTREILDAMNRDCG.PL. |
Retrocopy | EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS |
|
Parental | HLQVDGGMTNNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLDPEDLSAVTVERFEPQ |
| HLQVDGGMTNNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSL.PEDLSAVT.ERFEPQ |
Retrocopy | HLQVDGGMTNNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLKPEDLSAVTMERFEPQ |
|
Parental | INAEESEIRYSTWKKAVMKSMGWVTTQSSESGMP |
| INA.ESEIRYSTWKKAV.KSMGWVTTQ..E.G.P |
Retrocopy | INAKESEIRYSTWKKAVKKSMGWVTTQYPENGDP |
|
Legend:
* | Stop codon |
> | Forward frameshift by one nucleotide |
< | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
Library |
Retrocopy expression |
Parental gene expression |
SRP014902_placenta |
0 .00 RPM |
4 .25 RPM |
SRP014902_testis |
0 .00 RPM |
2 .55 RPM |
SRP018288_heart |
0 .00 RPM |
30 .04 RPM |
SRP018288_kidney |
0 .10 RPM |
184 .80 RPM |
SRP018288_liver |
0 .16 RPM |
110 .82 RPM |
SRP018288_lung |
0 .20 RPM |
20 .67 RPM |
SRP018856_adipose |
0 .00 RPM |
22 .26 RPM |
SRP035408_brain |
0 .32 RPM |
4 .83 RPM |
SRP035408_liver |
0 .00 RPM |
94 .14 RPM |
Sus scrofa was not studied using ChIP-Seq data.
3 EST(s) were mapped to retro_sscr_479 retrocopy
EST ID |
Start |
End |
Identity |
Match |
Mis-match |
Score |
CV871274 |
138071607 |
138072264 |
100 |
657 |
0 |
657 |
CV875376 |
138071584 |
138072214 |
99.6 |
627 |
3 |
624 |
CX063319 |
138071595 |
138072190 |
99 |
589 |
6 |
583 |
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_479 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_479 has 0 orthologous retrocopies within eutheria group .
Parental genes homology:
Parental genes homology involve
7 parental genes, and
10 retrocopies.