RetrogeneDB ID: retro_mdom_1682

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:184315553..184316431(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCMF1
• Ensembl ID: ENSMODG00000015567
• Aliases: None
• Description: potassium channel modulatory factor 1 [Source:HGNC Symbol;Acc:20589]

Sequence

>retro_mdom_1682
GAGACGTCTCTTCAAGAACATGTTACTTCTGAACACGCAGAAACATCAACAGAAGTGATTTGTCCAATCTGTGCAGCATT
ACCTGGCGGAGATCCTAATCATGTCACAGATGACTTTGCAGCTCATTTCACACTTGAACACAGAGCCCCTAGAGATTTAG
ATGAATCGAGTGGTGTTCGCCATGTCCGTAGAATGTTTCACCCTGGCCGAGGGCTAGGAGGTCCTCGGGCCCGTCGATCA
AGCATGCACTTTACTAGCAGTACTACTACTGGTGGGCTTTCTTCTTCGCCGAGTTCATATTCTCCAAGCAATAGGGAAGC
TATGGATCCTATCGCTGAGCTTCTCTTTCAGCTCTCAGGAGTGCGACGTTCTGCGGGAGGATAGCTCAATTCCTCCAGTC
CTTCTGCCTCGCAGCTCCAGCAGCTGCAGATGCAGCTTCAGCTGGAACGAGAGCAGGCACAGGCAGCGCGCCAGCAGCTG
GAGACGGCCCGCAACGCCACCCGGGGCACGAACGCGAGCAGCGTCACCACGACAATTACACAATCGACAGCAACCACCAA
CACGACCAGTACGGAGAACTGTCAGCAAACTGTTCAGAACTCCCAGTTTCTCCTTACAAGGTTAGATGGCCCTAAGATGT
CCGAAACAGAACGTCAGTCAATGGAAAGCGAGCGGGCAGACCGTAGCCTGTTTGTCCAAGAGCTTCTACTGTCCACTTTG
ATGCGGGAAGAAAGTTCTTCCTCAGATGAGGATGAACGAGGGAAATTGCAGATTTTGGTGCTATGGGCTGTGTAAAGGCA
TAAGCCTTTAGATATTGCTTTAGAAAACCTAAATTAAAAGAGAGTAACAAAGGAAATGAGCCTCCGCCTCCTCCTCTT

Alignment

ORF - retro_mdom_1682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.28 %
• Parental protein coverage: 76.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ETSLQEHVTSEHAETSTEVICPICAALPGGDPNHVTDDFAAHLTLEHRAPRDLISFYSDGVRHVRRMFHP
          ETSLQEHVTSEHAETSTEVICPICAALPGGDPNHVTDDFAAH.TLEHRAPRDL....S.GVRHVRRMFHP
Retrocopy ETSLQEHVTSEHAETSTEVICPICAALPGGDPNHVTDDFAAHFTLEHRAPRDLDE--SSGVRHVRRMFHP

Parental  GRGLGGPRARRSNMHFTSSST-GGLSSSQSSYSPSNREAMDPIAELLSQLSGVRRSAGGQLNSSGPSASQ
          GRGLGGPRARRS.MHFTSS.T.GGLSSS.SSYSPSNREAMDPIAELL.QLSGVRRSAGG.LNSS.PSASQ
Retrocopy GRGLGGPRARRSSMHFTSSTTTGGLSSSPSSYSPSNREAMDPIAELLFQLSGVRRSAGG*LNSSSPSASQ

Parental  LQQLQMQLQLERQHAQAARQQLETARNATRRTNASSVTTTITQSTATTNTTSTENSQQTVQNSQFLLTRL
          LQQLQMQLQLER..AQAARQQLETARNATR.TNASSVTTTITQSTATTNTTSTEN.QQTVQNSQFLLTRL
Retrocopy LQQLQMQLQLEREQAQAARQQLETARNATRGTNASSVTTTITQSTATTNTTSTENCQQTVQNSQFLLTRL

Parental  NDPKMSETERQSMESERADRSLFVQELLLSTLMREESSSSDEDERG-EIADFGAMGCVDI-MPLDVALEN
          ..PKMSETERQSMESERADRSLFVQELLLSTLMREESSSSDEDERG.EIADFGAMGCV....PLD.ALEN
Retrocopy DGPKMSETERQSMESERADRSLFVQELLLSTLMREESSSSDEDERG<EIADFGAMGCVKA>KPLDIALEN

Parental  LN-LKESNKGNEPPPPPL
          LN.LKESNKGNEPPPPPL
Retrocopy LN<LKESNKGNEPPPPPL

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1682 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1682 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005786	1 retrocopy	retro_chof_1282,
Dasypus novemcinctus	ENSDNOG00000006752	2 retrocopies	retro_dnov_1000, retro_dnov_2063,
Echinops telfairi	ENSETEG00000001809	1 retrocopy	retro_etel_1685,
Myotis lucifugus	ENSMLUG00000000979	1 retrocopy	retro_mluc_1781,
Monodelphis domestica	ENSMODG00000015567	1 retrocopy	retro_mdom_1682 ,
Otolemur garnettii	ENSOGAG00000034863	2 retrocopies	retro_ogar_3140, retro_ogar_397,
Vicugna pacos	ENSVPAG00000010386	1 retrocopy	retro_vpac_650,