RetrogeneDB ID: retro_mdom_1894

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:280107748..280108422(+)
• Located in intron of: ENSMODG00000014789

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SURF2
• Ensembl ID: ENSMODG00000012766
• Aliases: None
• Description: surfeit 2 [Source:HGNC Symbol;Acc:11475]

Sequence

>retro_mdom_1894
GGCAGCACTGACGTCCAGGTGCCTCCAGATGTGCAGGATTTTCTCCACAGCCATCCCATGCTGCATTTGTGCTCTGGTGG
GGCCAAGGTAAGGTGCAGGCTGACAAGCCATGAACTACCCAGCCAACTGACAGCCCTCCAGGTCTACACCAGTGGTAAGA
AATAGCAGCTGATACACACCACCCAAAACTTTGACTACGAAGAGTTTGAGCCATACATTGTACCCAGCACCAAGAATCCA
CACCAGCTCTTCTGCAAACTCACCCTTCGGCATATCAACAGGCTTCCAGAGCATGTCCTACGTCATGTCCAGGGCTGGCA
CTACCAAAGGGCTCTGCACAAATATGAAGAATGTCAGAAGCAGGGTGTGGAGTATGTTCCAGCCTGCTTACTGCAAAGAG
AAGGAAATGGGAAGACTTGATTGATGGTGACCAGCAGCCGCCAAAAAAAGGATTTCTGGCAACCCAAATCCAGTGATGAA
GAAGACCAGAGTGATGAAGCATGACTGATTTATACCCACCGGAGCTGTTCTCTGAAAAGAGCCCAGGTAAAAATGGAGAT
GTCGCAGACATTGACAGACATTGAAGACAACAGCCTTCCAGGGAGAATGGTATCATGGGCAGAGGAGAGAAGATGGAGAT
GGGCAGGCCAACGTGTAATAAGAGGACAAAGCAG

Alignment

ORF - retro_mdom_1894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.88 %
• Parental protein coverage: 99.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSADAQVPPDVQDFLRGHPALQLCPGGTKVRCRLTGHELPSRLAPLQAYTSGKKYQRLMRTTQTFDYEEF
          GS.D.QVPPDVQDFL..HP.L.LC.GG.KVRCRLT.HELPS.L..LQ.YTSGKK.Q.L..TTQ.FDYEEF
Retrocopy GSTDVQVPPDVQDFLHSHPMLHLCSGGAKVRCRLTSHELPSQLTALQVYTSGKK*Q-LIHTTQNFDYEEF

Parental  EPHIVPSTKNPHQLFCKLTLRHINRLPDHVLRHVQGQRYQKALHKYEECQKQGVEYIPACLLQ-KRRKRE
          EP.IVPSTKNPHQLFCKLTLRHINRLP.HVLRHVQG..YQ.ALHKYEECQKQGVEY.PACLLQ.KRRK.E
Retrocopy EPYIVPSTKNPHQLFCKLTLRHINRLPEHVLRHVQGWHYQRALHKYEECQKQGVEYVPACLLQ<KRRKWE

Parental  DLIDSDQQP-RKKDFWQPESSDEEDQSDD-SMTDLYPPELFSEKNPGKNGDVEGSYLTDNEDNTQPSREN
          DLID.DQQP..KKDFWQP.SSDEEDQSD..SMTDLYPPELFSEK.PGKNGDV......D.....QPSREN
Retrocopy DLIDGDQQP>QKKDFWQPKSSDEEDQSDE<SMTDLYPPELFSEKSPGKNGDVAD---IDRH*RQQPSREN

Parental  GIVGRGEKMEVDRPICNKRTKK
          GI.GRGEKME..RP.CNKRTK.
Retrocopy GIMGRGEKMEMGRPTCNKRTKQ

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	60.91 RPM
SRP007412_cerebellum	0.00 RPM	61.37 RPM
SRP007412_heart	0.00 RPM	119.81 RPM
SRP007412_kidney	0.00 RPM	201.48 RPM
SRP007412_liver	0.00 RPM	216.00 RPM
SRP007412_testis	0.00 RPM	52.45 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1894 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1894 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019763	1 retrocopy	retro_cfam_1702,
Callithrix jacchus	ENSCJAG00000009532	5 retrocopies	retro_cjac_3362, retro_cjac_3452, retro_cjac_3606, retro_cjac_3648, retro_cjac_3914,
Felis catus	ENSFCAG00000028927	1 retrocopy	retro_fcat_277,
Monodelphis domestica	ENSMODG00000012766	1 retrocopy	retro_mdom_1894 ,