RetrogeneDB ID: | retro_mdom_514 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 1:121263345..121264517(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000019446 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CDH13 | ||
| Ensembl ID: | ENSMODG00000015029 | ||
| Aliases: | None | ||
| Description: | cadherin 13, H-cadherin (heart) [Source:HGNC Symbol;Acc:1753] |
Retrocopy-Parental alignment summary:
>retro_mdom_514
ACTCTGGAAAACCCTAAATATGAACTGATCATTGAAGCTCAGGACATGGCTGGTTTGGACGTTGGTTTAACTGGGACAGC
AACAGCTACCATTCTGATTGATGACAAAAATGATCACTCCCCAAAGTTCACCAAGAAAGAGTTTCATGCCATTGTCAATG
AAGGAGTTGTGGGAGTGATTGTCAATTTAACAGTCCAAGATAAGGATGACCCTACTACTGCAGTCTGGAGAGCAGTCTAC
ACTATCATCAATGGAAATCCAGGGCAAAGTTTTGAAATACATACGAATCCCCAAACCAACGAGGGAATGCTTTCTGTTGT
CAAACCTTTGGATTATGAGATTTCAGCATTTCACACACTATTGATCAAAGTAGAAAATGAAGACCCATTGGTTCTTGATG
TAGCATATGCCCCAGCTCTACAGCCACAGTCCAGATAACTGTCTCGGATGTAAATGAAGGCCCAGTTTTTCACCCTGACC
CCATGACAGTGACCAAGCGTGAGAACATCACTATTGGCAGCATGCTGTTGACAGTAAATGCCACAGATCCTGATTCCTTG
CAGCATCAGACCATTAGGTACTCTATTTATAAAGATCCAGTAGGATGGCTATACATCAACCCAATCAATGGGACAATTGA
TACAGCAGCTGTCTTGGACCGTGAATCTCCATTTGTCCACAATAATATATACACTGCACTTTTCCTTGCAATAGATAGTG
GTGATCCTCCTGCAACTGGCACTGGAACTCTACAGATAAAACTGGAAGATGTGAATGACAATGCTCCTCTTATTTACCCC
ACACTTGCCAAAGTTTGTGATGATGCCAGAGATCTCAATGTGGTCATTCTGGGTGCATCAGATAAGGATCTCCACCCAAA
TACTGATCCATTCAAATTTGAATTGAATAAACAAACTGGGTCTGATAAATTCTGGAAAATTTCTAAGATCAATGACACTC
ATGCCCAGGTAAGCCTTCTTCAGAACCTGAAGAAAGCCAACTACAAACTACCTGTCATGGTGACAGACTCGGGCACGCCA
CCTTTGTCAAACACCACAGAACTAAGAGTGCAAGTTTGTTCCTGTAAGAAATCTAAAATGGACTGCAGCTCAGCTGGGAT
CCCGCATATCAGAACCACCTTAGTTCTGCTTCTTTCATTCTTCAGCTTAGTA
ORF - retro_mdom_514 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.7 % |
| Parental protein coverage: | 59.42 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | TLENPKYELIIEAQDMAGLDVGLTGTATATILIDDKNDHSPKFTKKEFHATVNEGVVGVIVNLTVEDKDD |
| TLENPKYELIIEAQDMAGLDVGLTGTATATILIDDKNDHSPKFTKKEFHA.VNEGVVGVIVNLTV.DKDD | |
| Retrocopy | TLENPKYELIIEAQDMAGLDVGLTGTATATILIDDKNDHSPKFTKKEFHAIVNEGVVGVIVNLTVQDKDD |
| Parental | PTTAAWRAVYTIINGNPGQSFEIHTNPQTNEGMLSVVKPLDYEISAFHTLLIKVENEDPLVPDVAYGP-S |
| PTTA.WRAVYTIINGNPGQSFEIHTNPQTNEGMLSVVKPLDYEISAFHTLLIKVENEDPLV.DVAY.P.S | |
| Retrocopy | PTTAVWRAVYTIINGNPGQSFEIHTNPQTNEGMLSVVKPLDYEISAFHTLLIKVENEDPLVLDVAYAP<S |
| Parental | STATVQITVSDVNEGPVFHPDPMTVTKRENITIGSMLLTVNATDPDSLQHQTIRYSIYKDPAGWLYINPI |
| STATVQITVSDVNEGPVFHPDPMTVTKRENITIGSMLLTVNATDPDSLQHQTIRYSIYKDP.GWLYINPI | |
| Retrocopy | STATVQITVSDVNEGPVFHPDPMTVTKRENITIGSMLLTVNATDPDSLQHQTIRYSIYKDPVGWLYINPI |
| Parental | NGTIDTAAVLDRESPFVHNNIYTALFLAIDSGDPPATGTGTLQIKLEDVNDNAPLIYPTLAKVCDDAKDL |
| NGTIDTAAVLDRESPFVHNNIYTALFLAIDSGDPPATGTGTLQIKLEDVNDNAPLIYPTLAKVCDDA.DL | |
| Retrocopy | NGTIDTAAVLDRESPFVHNNIYTALFLAIDSGDPPATGTGTLQIKLEDVNDNAPLIYPTLAKVCDDARDL |
| Parental | NVVILGASDKDLHPNTDPFKFELNKQTGSDKFWKISKINDTHAQVSLLQNLKKANYNLPVMVTDSGTPPL |
| NVVILGASDKDLHPNTDPFKFELNKQTGSDKFWKISKINDTHAQVSLLQNLKKANY.LPVMVTDSGTPPL | |
| Retrocopy | NVVILGASDKDLHPNTDPFKFELNKQTGSDKFWKISKINDTHAQVSLLQNLKKANYKLPVMVTDSGTPPL |
| Parental | SNTTELRVQVCSCKKSKMDCSSAGIPHIRTTLVLLLSFFSLV |
| SNTTELRVQVCSCKKSKMDCSSAGIPHIRTTLVLLLSFFSLV | |
| Retrocopy | SNTTELRVQVCSCKKSKMDCSSAGIPHIRTTLVLLLSFFSLV |
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 |
|---|---|---|
| SRP007412_brain | 0 .12 RPM | 86 .78 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 63 .33 RPM |
| SRP007412_heart | 0 .40 RPM | 408 .27 RPM |
| SRP007412_kidney | 0 .00 RPM | 14 .49 RPM |
| SRP007412_liver | 0 .00 RPM | 1 .01 RPM |
| SRP007412_testis | 0 .00 RPM | 24 .55 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_514 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_514 was not experimentally validated.
Retrocopy orthology:
Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000015029 | 1 retrocopy |
retro_mdom_514 ,
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