RetrogeneDB ID: retro_mdom_138

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:269727830..269729909(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000009766
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000001962
• Aliases: None
• Description: None

Sequence

>retro_mdom_138
ATGGCAGAAAAGTTTGAAAGTCTCATGAACATTCATGGTTTTGATCTGGGCTCTCGGTATATGGACTTAAAACCGCTGGG
TTGTGGTGGCAATGGCTTAGTTTTTTCTGCTGTCGATAATGACTGTGACAAAAGAGTGGCTGTCAAGAAAATTGTTCTTA
CAGATCCCCAGAGTGTTAAACATGCTTTACGCGAAATCAAAATTATTAGAAGACTCGACCATGATAACATTGTGAAAGTA
TTTGAAATTCTTGGTCCCAGTGGAAGCCAGTTAACAGATGATGTGGGCTCTCTGACAGAACTGAACAGTGTTTACATTGT
TCAGGAGTACATGGAGACAGACTTGGCTAATCTGCTAGAGCAGGGCCCTTTATTGGAGGAGCATGCCAGGCTTTTCATGT
ATCAGCTGCTACGTGGGCTCAAGTATATTCATTCTGCAAATGTACTGCACAGAGATCTCAAACCAGCTAATCTTTTCATT
AATACCGAAGACTTGGTGCTGAAGATAGGTGACTTTGGTCTTGCCCGGATCATGGATCCCCATTATTCCCACAAGGGTCA
TCTTTCTGAAGGATTGGTTACTAAATGGTACAGATCTCCACGACTTTTACTTTCTCCTAATAACTATACTAAAGCCATTG
ATATGTGGGCTGCAGGATGCATCTTTGCTGAAATGCTGACTGGGAAAACCCTCTTTGCAGGTGCACATGAACTTGAACAG
ATGCAACTGATTTTAGAATCTATTCCTGTTGTACATGAGGAAGATCGTCAGGAGCTTCTCAGTGTAATCCCAGTTTACAT
AAAAAATGATATGACTGAGCCACACAAACCCTTAACTCAGCTGCTTCCAGGAATTAGTCGTGAAGCACTGGACTTCCTGG
AACAAATTTTGACATTTAGTCCCATGGATCGATTGACCGCAGAAGAAGCTCTGTCCCATCCTTATATGAGCATTTATTCC
TTTCCAATGGATGAACCAATTTCAAGCCATCCTTTTCACATTGAAGATGAAGTTGATGATATTTTGCTCATGGATGAAAC
TCATAGTCATATTTATAATTGGGAGAGGTACCATGATTGTCAGTTTTCAGACCATGACTGGCCTATACATAATAATTTTG
ATATTGAAGAAGTTCAGCGTGACCCAAGGGCTCTTTCTGATGTCACTGATGAAGAGGAAGTCCAAGTAGATCCTCGAAAA
TATTTGGATGGAGATCGTGAAAAGTATCTGAAGGATCCTGCCTTTGATACCCATTTCTCTACTGAGCCTTGTTGGCAATA
TCCAGATCATCATGAAAACAAGTATTGTGATCTGGAATGCAGCCACACTTGTAACTACAAAATGAGGTCGTCATCATATC
TAGATAACTTAGTTTGGAGAGAGAGTGAAGTTAACCATTACTATGAACCCAAACTTATTATAGATCTTTCTAATTGGAAA
GAACAAAGCAAAGAAAAATCTGATAAGAAAGGCAAGTCAAAATGTGAAAGGAATGGATTGGTTAAAGCTCAAATAGCTCT
TGAGGAAGCATCACAGCAACTGGTTGAAAAAGAAAGGGAGAAGAATCAAGGATTTGACTTTGATTCCTTTATTGCAGGAA
CTATTCAACTTAGTTCACAACATGAGTCTACTGATGTTGTTGATAAATTAAATGACTTGAATAGCTCAGTGTCCCAACTA
GAATTGAAAAGTTTGATATCAAAGTCAGTAAGCCGGGAAAAACAGGAAAAAGGAATGGCGAATTTGGCTCAGTTAGAAGC
TTTGTACCAGTCTTCTTGGGACAGCCAGTTTGTGAGTGGTGGGGAGGAATGTTTTCTCATAGATCAGTTTTGTTGTGAAG
TAAGAAAGGATGAACAGATTGAGAAGGAAAACACTTACACCAGTTACTTGGACAAGTTCTTTAGCAGGAAGGAAGATACT
GAAATGCTAGAAACTGAGCCAATAGAGGATGGCAAGTTTGGGGAAAGAGAAAGTGAGGAGGGTTTTCTTAACAATAGTGG
GGAGTTCCTCTTTAACAAGCAGCTTGAGTCTATAGGCATCCCACAGTTTCATAGTCCAGTTGGTTCACCACNAAAATAG

Alignment

ORF - retro_mdom_138 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.86 %
• Parental protein coverage: 95.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEKFESLMNIHGFDLGSRYMDLKPLGCGGNGLVFSAVDNDCDKRVAVKKIVLTDPQSVKHALREIKIIR
          MAEKFESLMNIHGFDLGSRYMDLKPLGCGGNGLVFSAVDNDCDKRVAVKKIVLTDPQSVKHALREIKIIR
Retrocopy MAEKFESLMNIHGFDLGSRYMDLKPLGCGGNGLVFSAVDNDCDKRVAVKKIVLTDPQSVKHALREIKIIR

Parental  RLDHDNIVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANLLEQGPLLEEHARLFMYQLLRGL
          RLDHDNIVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANLLEQGPLLEEHARLFMYQLLRGL
Retrocopy RLDHDNIVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANLLEQGPLLEEHARLFMYQLLRGL

Parental  KYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNYT
          KYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNYT
Retrocopy KYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNYT

Parental  KAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIKNDMTEPHKPLTQ
          KAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIKNDMTEPHKPLTQ
Retrocopy KAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIKNDMTEPHKPLTQ

Parental  LLPGISREALDFLEQILTFSPMDRLTAEEALSHPYMSIYSFPMDEPISSHPFHIEDEVDDILLMDETHSH
          LLPGISREALDFLEQILTFSPMDRLTAEEALSHPYMSIYSFPMDEPISSHPFHIEDEVDDILLMDETHSH
Retrocopy LLPGISREALDFLEQILTFSPMDRLTAEEALSHPYMSIYSFPMDEPISSHPFHIEDEVDDILLMDETHSH

Parental  IYNWERYHDCQFSDHDWPIHNNFDIEEVQRDPRALSDVTDEEEVQVDPRKYLDGDREKYLKDPAFDTHFS
          IYNWERYHDCQFSDHDWPIHNNFDIEEVQRDPRALSDVTDEEEVQVDPRKYLDGDREKYLKDPAFDTHFS
Retrocopy IYNWERYHDCQFSDHDWPIHNNFDIEEVQRDPRALSDVTDEEEVQVDPRKYLDGDREKYLKDPAFDTHFS

Parental  TEPCWQYPDHHENKYCDLECSHTCNYKMRSSSYLDNLVWRESEVNHYYEPKLIIDLSNWKEQSKEKSDKK
          TEPCWQYPDHHENKYCDLECSHTCNYKMRSSSYLDNLVWRESEVNHYYEPKLIIDLSNWKEQSKEKSDKK
Retrocopy TEPCWQYPDHHENKYCDLECSHTCNYKMRSSSYLDNLVWRESEVNHYYEPKLIIDLSNWKEQSKEKSDKK

Parental  GKSKCERNGLVKAQIALEEASQQLVEKEREKNQGFDFDSFIAGTIQLSSQHESTDVVDKLNDLNSSVSQL
          GKSKCERNGLVKAQIALEEASQQLVEKEREKNQGFDFDSFIAGTIQLSSQHESTDVVDKLNDLNSSVSQL
Retrocopy GKSKCERNGLVKAQIALEEASQQLVEKEREKNQGFDFDSFIAGTIQLSSQHESTDVVDKLNDLNSSVSQL

Parental  ELKSLISKSVSREKQEKGMANLAQLEALYQSSWDSQFVSGGEECFLIDQFCCEVRKDEQIEKENTYTSYL
          ELKSLISKSVSREKQEKGMANLAQLEALYQSSWDSQFVSGGEECFLIDQFCCEVRKDEQIEKENTYTSYL
Retrocopy ELKSLISKSVSREKQEKGMANLAQLEALYQSSWDSQFVSGGEECFLIDQFCCEVRKDEQIEKENTYTSYL

Parental  DKFFSRKEDTEMLETEPIEDGKFGERESEEGFLNNSGEFLFNKQLESIGIPQFHSPVGSPLK
          DKFFSRKEDTEMLETEPIEDGKFGERESEEGFLNNSGEFLFNKQLESIGIPQFHSPVGSP.K
Retrocopy DKFFSRKEDTEMLETEPIEDGKFGERESEEGFLNNSGEFLFNKQLESIGIPQFHSPVGSPXK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	14.30 RPM
SRP007412_cerebellum	0.00 RPM	12.73 RPM
SRP007412_heart	0.00 RPM	4.78 RPM
SRP007412_kidney	0.00 RPM	2.63 RPM
SRP007412_liver	0.00 RPM	9.57 RPM
SRP007412_testis	0.00 RPM	6.48 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_138 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_138 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000962	1 retrocopy	retro_cjac_2633,
Homo sapiens	ENSG00000069956	2 retrocopies	retro_hsap_1257, retro_hsap_2519,
Gorilla gorilla	ENSGGOG00000004003	1 retrocopy	retro_ggor_1571,
Monodelphis domestica	ENSMODG00000001962	2 retrocopies	retro_mdom_138 , retro_mdom_63,
Monodelphis domestica	ENSMODG00000017722	1 retrocopy	retro_mdom_101,
Nomascus leucogenys	ENSNLEG00000006476	2 retrocopies	retro_nleu_1441, retro_nleu_2095,
Otolemur garnettii	ENSOGAG00000030786	1 retrocopy	retro_ogar_1827,
Pongo abelii	ENSPPYG00000006482	2 retrocopies	retro_pabe_1853, retro_pabe_3322,
Pan troglodytes	ENSPTRG00000020224	3 retrocopies	retro_ptro_1464, retro_ptro_2743, retro_ptro_3045,
Sarcophilus harrisii	ENSSHAG00000017091	1 retrocopy	retro_shar_445,
Sus scrofa	ENSSSCG00000004624	1 retrocopy	retro_sscr_162,
Tupaia belangeri	ENSTBEG00000007876	2 retrocopies	retro_tbel_1879, retro_tbel_2946,
Tursiops truncatus	ENSTTRG00000016253	2 retrocopies	retro_ttru_322, retro_ttru_75,