RetrogeneDB ID: | retro_btau_211 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 6:28075089..28075890(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000023000 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DFFA | ||
| Ensembl ID: | ENSBTAG00000013535 | ||
| Aliases: | None | ||
| Description: | DNA fragmentation factor subunit alpha [Source:RefSeq peptide;Acc:NP_001068810] |
Retrocopy-Parental alignment summary:
>retro_btau_211
ATGGAGGTGGCCAGCAGCCCTGCAGCTCCAGAACCCGGCGAGATCTGGGCTCTAAAGCAGTGTCTGCTGCGCTGCAACAA
CAGCCGCGAACAGCACGGCATGGCAGCCTCATGCCTCGAGGAGCTGAGGAACAAGGCTTCTGACATTCTGGCCATCGATA
AGTCCCAGGCGCCAGTCACCCTGGTCCTGGAAGAGGATGGCACCATAGTGGATGACTATGATTACTTCCTGTGTCTTCCT
GCCAATACTAAGTTTGTGGCATTGGCTGGGAATGAGAAGTGGACACACAATTCAGATGGAGGTACAGCTTGGATAACCCA
AGAGTCCTTCCACAGAGATGAAACAGACAGCGGGGCAGGGCTGAAGTGGAAGAACGTGGCCAGGCAGCTGAAGGAAGACC
TATCCAGCATCATCCTGATGTCCAAGGAGGAGCTCCAGATGCTCACTGATGACCCATGTTCGGAGCTGCCTCAGGAACTC
GGCCAAAATCATGTGGTAGTCCAGGGGCTCCAGAACACCCTCCAGCAGGTGCTTGACCAGAAAGAGGAAGCCCGTCAGTC
CAGACAGCTCGTGGAACTTTACCTCCAAGCTTTGGAGAAGGAAGGCAGCATCTTGTTGAAGCAGCAAGAGTCCAGAGCTG
ACCTCGGGGATGAAAGGGACGCTGCTGAGACGGGCGTTAGAAAGCGCTCCTCAGACATTATGCCTGCAAGCCAGATCCTC
TTAGTGCTAAAGGAGAAATCTGCCCCAGAGCTGAGTTTGTCTGGTCCGGATCTGGAAGTGGGCAAGCACCAGGGACCCTG
A
ORF - retro_btau_211 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.33 % |
| Parental protein coverage: | 80.85 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MEVPGGPAAPEPGEIRALKQCLLRRNKSREQHGVAASCLKELRNKACDILAIDKSLAPVTLVLAEDGTIV |
| MEV...PAAPEPGEI.ALKQCLLR.N.SREQHG.AASCL.ELRNKA.DILAIDKS.APVTLVL.EDGTIV | |
| Retrocopy | MEVASSPAAPEPGEIWALKQCLLRCNNSREQHGMAASCLEELRNKASDILAIDKSQAPVTLVLEEDGTIV |
| Parental | DDDDYFLCLPANTKFVVLAGNEKWTHNSDGGTAWITQESFDRDETDSGAGLKWKNVARQLKEDLSSIILL |
| DD.DYFLCLPANTKFV.LAGNEKWTHNSDGGTAWITQESF.RDETDSGAGLKWKNVARQLKEDLSSIIL. | |
| Retrocopy | DDYDYFLCLPANTKFVALAGNEKWTHNSDGGTAWITQESFHRDETDSGAGLKWKNVARQLKEDLSSIILM |
| Parental | SEEELQMLIDVPCSELAQELSQSHVAVQGLQNTLQQVLDQREEARQSRQLLELYLRALEKEGGILSKQQE |
| S.EELQML.D.PCSEL.QEL.Q.HV.VQGLQNTLQQVLDQ.EEARQSRQL.ELYL.ALEKEG.IL.KQQE | |
| Retrocopy | SKEELQMLTDDPCSELPQELGQNHVVVQGLQNTLQQVLDQKEEARQSRQLVELYLQALEKEGSILLKQQE |
| Parental | SRADLGDESDAVDTGIRESFSEVTPASQILLALKEKPAPELSLSSQDLELVAKEDP |
| SRADLGDE.DA..TG.R...S...PASQILL.LKEK.APELSLS..DLE......P | |
| Retrocopy | SRADLGDERDAAETGVRKRSSDIMPASQILLVLKEKSAPELSLSGPDLEVGKHQGP |
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 |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 10 .81 RPM |
| ERP005899_muscle | 0 .05 RPM | 16 .58 RPM |
| SRP017611_brain | 0 .00 RPM | 14 .57 RPM |
| SRP017611_kidney | 0 .00 RPM | 20 .69 RPM |
| SRP017611_liver | 0 .00 RPM | 9 .51 RPM |
| SRP030211_testis | 0 .03 RPM | 4 .51 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_211 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_211 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_211 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000013535 | 1 retrocopy |
retro_btau_211 ,
|
| Homo sapiens | ENSG00000160049 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000012721 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000001899 | 1 retrocopy |